def build(mol,
ff=None,
topo=None,
param=None,
prefix='structure',
outdir='./build',
caps=None,
ionize=True,
saltconc=0,
saltanion=None,
saltcation=None,
disulfide=None,
tleap=None,
execute=True,
atomtypes=None,
offlibraries=None,
gbsa=False,
igb=2):
""" Builds a system for AMBER
Uses tleap to build a system for AMBER. Additionally it allows the user to ionize and add disulfide bridges.
Parameters
----------
mol : :class:`Molecule <htmd.molecule.molecule.Molecule>` object
The Molecule object containing the system
ff : list of str
A list of leaprc forcefield files.
Use :func:`amber.listFiles <htmd.builder.amber.listFiles>` to get a list of available forcefield files.
Default: :func:`amber.defaultFf <htmd.builder.amber.defaultFf>`
topo : list of str
A list of topology `prepi/prep/in` files.
Use :func:`amber.listFiles <htmd.builder.amber.listFiles>` to get a list of available topology files.
Default: :func:`amber.defaultTopo <htmd.builder.amber.defaultTopo>`
param : list of str
A list of parameter `frcmod` files.
Use :func:`amber.listFiles <htmd.builder.amber.listFiles>` to get a list of available parameter files.
Default: :func:`amber.defaultParam <htmd.builder.amber.defaultParam>`
prefix : str
The prefix for the generated pdb and psf files
outdir : str
The path to the output directory
Default: './build'
caps : dict
A dictionary with keys segids and values lists of strings describing the caps for a particular protein segment.
e.g. caps['P'] = ['ACE', 'NME'] or caps['P'] = ['none', 'none']. Default: will apply ACE and NME caps to every
protein segment.
ionize : bool
Enable or disable ionization
saltconc : float
Salt concentration to add to the system after neutralization.
saltanion : {'Cl-'}
The anion type. Please use only AMBER ion atom names.
saltcation : {'Na+', 'K+', 'Cs+'}
The cation type. Please use only AMBER ion atom names.
disulfide : list of pairs of atomselection strings
If None it will guess disulfide bonds. Otherwise provide a list pairs of atomselection strings for each pair of
residues forming the disulfide bridge.
tleap : str
Path to tleap executable used to build the system for AMBER
execute : bool
Disable building. Will only write out the input script needed by tleap. Does not include ionization.
atomtypes : list of triplets
Custom atom types defined by the user as ('type', 'element', 'hybrid') triplets
e.g. (('C1', 'C', 'sp2'), ('CI', 'C', 'sp3')). Check `addAtomTypes` in AmberTools docs.
offlibraries : str or list
A path or a list of paths to OFF library files. Check `loadOFF` in AmberTools docs.
gbsa : bool
Modify radii for GBSA implicit water model
igb : int
GB model. Select: 1 for mbondi, 2 and 5 for mbondi2, 7 for bondi and 8 for mbondi3.
Check section 4. The Generalized Born/Surface Area Model of the AMBER manual.
Returns
-------
molbuilt : :class:`Molecule <htmd.molecule.molecule.Molecule>` object
The built system in a Molecule object
Example
-------
>>> from htmd.ui import * # doctest: +SKIP
>>> mol = Molecule("3PTB")
>>> molbuilt = amber.build(mol, outdir='/tmp/build') # doctest: +SKIP
>>> # More complex example
>>> disu = [['segid P and resid 157', 'segid P and resid 13'], ['segid K and resid 1', 'segid K and resid 25']]
>>> molbuilt = amber.build(mol, outdir='/tmp/build', saltconc=0.15, disulfide=disu) # doctest: +SKIP
"""
# Remove pdb protein bonds as they can be regenerated by tleap. Keep non-protein bonds i.e. for ligands
mol = mol.copy()
_removeProteinBonds(mol)
if tleap is None:
tleap = _findTleap()
else:
if shutil.which(tleap) is None:
raise NameError(
'Could not find executable: `{}` in the PATH. Cannot build for AMBER.'
.format(tleap))
if not os.path.isdir(outdir):
os.makedirs(outdir)
_cleanOutDir(outdir)
if ff is None:
ff = defaultFf()
if topo is None:
topo = defaultTopo()
if param is None:
param = defaultParam()
if caps is None:
caps = _defaultProteinCaps(mol)
_missingSegID(mol)
_checkMixedSegment(mol)
mol = _charmmLipid2Amber(mol)
_applyProteinCaps(mol, caps)
f = open(os.path.join(outdir, 'tleap.in'), 'w')
f.write('# tleap file generated by amber.build\n')
# Printing out the forcefields
if isinstance(ff, str):
ff = [ff]
for i, force in enumerate(ff):
if not os.path.isfile(force):
force = _locateFile(force, 'ff', tleap)
if force is None:
continue
newname = 'ff{}_{}'.format(i, os.path.basename(force))
shutil.copy(force, os.path.join(outdir, newname))
f.write('source {}\n'.format(newname))
f.write('\n')
if gbsa:
gbmodels = {
1: 'mbondi',
2: 'mbondi2',
5: 'mbondi2',
7: 'bondi',
8: 'mbondi3'
}
f.write('set default PBradii {}\n\n'.format(gbmodels[igb]))
# Adding custom atom types
if atomtypes is not None:
atomtypes = ensurelist(tocheck=atomtypes[0], tomod=atomtypes)
f.write('addAtomTypes {\n')
for at in atomtypes:
if len(at) != 3:
raise RuntimeError(
'Atom type definitions have to be triplets. Check the AMBER documentation.'
)
f.write(' {{ "{}" "{}" "{}" }}\n'.format(at[0], at[1], at[2]))
f.write('}\n\n')
# Loading OFF libraries
if offlibraries is not None:
offlibraries = ensurelist(offlibraries)
for off in offlibraries:
if not os.path.isfile(off):
raise RuntimeError(
'Could not find off-library in location {}'.format(off))
newname = 'offlib{}_{}'.format(i, os.path.basename(off))
shutil.copy(off, os.path.join(outdir, newname))
f.write('loadoff {}\n'.format(newname))
# Loading frcmod parameters
f.write('# Loading parameter files\n')
for i, p in enumerate(param):
if not os.path.isfile(p):
p = _locateFile(p, 'param', tleap)
if p is None:
continue
newname = 'param{}_{}'.format(i, os.path.basename(p))
shutil.copy(p, os.path.join(outdir, newname))
f.write('loadamberparams {}\n'.format(newname))
f.write('\n')
# Loading prepi topologies
f.write('# Loading prepi topologies\n')
for i, t in enumerate(topo):
if not os.path.isfile(t):
t = _locateFile(t, 'topo', tleap)
if t is None:
continue
newname = 'topo{}_{}'.format(i, os.path.basename(t))
shutil.copy(t, os.path.join(outdir, newname))
f.write('loadamberprep {}\n'.format(newname))
f.write('\n')
f.write('# Loading the system\n')
f.write('mol = loadpdb input.pdb\n\n')
if np.sum(mol.atomtype != '') != 0:
logger.debug('Writing mol2 files for input to tleap.')
segs = np.unique(mol.segid[mol.atomtype != ''])
combstr = 'mol = combine {mol'
for s in segs:
name = 'segment{}'.format(s)
mol2name = os.path.join(outdir, '{}.mol2'.format(name))
mol.write(mol2name, (mol.atomtype != '') & (mol.segid == s))
if not os.path.isfile(mol2name):
raise NameError(
'Could not write a mol2 file out of the given Molecule.')
f.write('# Loading the rest of the system\n')
f.write('{} = loadmol2 {}.mol2\n\n'.format(name, name))
combstr += ' {}'.format(name)
combstr += '}\n\n'
f.write(combstr)
# Write patches for disulfide bonds (only after ionizing)
if not ionize:
# TODO: Remove this once we deprecate the class
from htmd.builder.builder import DisulfideBridge
from htmd.molecule.molecule import UniqueResidueID
if disulfide is not None and len(disulfide) != 0 and isinstance(
disulfide[0], DisulfideBridge):
newdisu = []
for d in disulfide:
r1 = UniqueResidueID.fromMolecule(
mol, 'resid {} and segname {}'.format(d.resid1, d.segid1))
r2 = UniqueResidueID.fromMolecule(
mol, 'resid {} and segname {}'.format(d.resid2, d.segid2))
newdisu.append([r1, r2])
disulfide = newdisu
# TODO: Remove up to here ----------------------
if disulfide is not None and len(disulfide) != 0 and isinstance(
disulfide[0][0], str):
disulfide = convertDisulfide(mol, disulfide)
if disulfide is None:
logger.info('Detecting disulfide bonds.')
disulfide = detectDisulfideBonds(mol)
# Fix structure to match the disulfide patching
if len(disulfide) != 0:
torem = np.zeros(mol.numAtoms, dtype=bool)
f.write('# Adding disulfide bonds\n')
for d in disulfide:
# Rename the residues to CYX if there is a disulfide bond
atoms1 = d[0].selectAtoms(mol, indexes=False)
atoms2 = d[1].selectAtoms(mol, indexes=False)
mol.resname[atoms1] = 'CYX'
mol.resname[atoms2] = 'CYX'
# Remove (eventual) HG hydrogens on these CYS (from proteinPrepare)
torem |= (atoms1 & (mol.name == 'HG')) | (atoms2 &
(mol.name == 'HG'))
# Convert to stupid amber residue numbering
uqseqid = sequenceID(
(mol.resid, mol.insertion, mol.segid)) + mol.resid[0]
uqres1 = int(np.unique(uqseqid[atoms1]))
uqres2 = int(np.unique(uqseqid[atoms2]))
f.write('bond mol.{}.SG mol.{}.SG\n'.format(uqres1, uqres2))
f.write('\n')
mol.remove(torem, _logger=False)
f.write('# Writing out the results\n')
f.write('saveamberparm mol ' + prefix + '.prmtop ' + prefix + '.crd\n')
f.write('quit')
f.close()
# Printing and loading the PDB file. AMBER can work with a single PDB file if the segments are separate by TER
logger.debug('Writing PDB file for input to tleap.')
pdbname = os.path.join(outdir, 'input.pdb')
# mol2 files have atomtype, here we only write parts not coming from mol2
# We need to write the input.pdb at the end since we modify the resname for disulfide bridges in mol
mol.write(pdbname, mol.atomtype == '')
if not os.path.isfile(pdbname):
raise NameError(
'Could not write a PDB file out of the given Molecule.')
molbuilt = None
if execute:
# Source paths of extra dirs (our dirs, not amber default)
htmdamberdir = os.path.abspath(
os.path.join(home(), 'builder', 'amberfiles'))
sourcepaths = [htmdamberdir]
sourcepaths += [
os.path.join(htmdamberdir, os.path.dirname(f)) for f in ff
if os.path.isfile(os.path.join(htmdamberdir, f))
]
extrasource = []
for p in sourcepaths:
extrasource.append('-I')
extrasource.append('{}'.format(p))
logpath = os.path.abspath(os.path.join(outdir, 'log.txt'))
logger.info('Starting the build.')
currdir = os.getcwd()
os.chdir(outdir)
f = open(logpath, 'w')
try:
cmd = [tleap, '-f', './tleap.in']
cmd[1:1] = extrasource
call(cmd, stdout=f)
except:
raise NameError('tleap failed at execution')
f.close()
errors = _logParser(logpath)
os.chdir(currdir)
if errors:
raise BuildError(errors + [
'Check {} for further information on errors in building.'.
format(logpath)
])
logger.info('Finished building.')
if os.path.exists(os.path.join(outdir, 'structure.crd')) and \
os.path.getsize(os.path.join(outdir, 'structure.crd')) != 0 and \
os.path.getsize(os.path.join(outdir, 'structure.prmtop')) != 0:
molbuilt = Molecule(os.path.join(outdir, 'structure.prmtop'))
molbuilt.read(os.path.join(outdir, 'structure.crd'))
else:
raise BuildError(
'No structure pdb/prmtop file was generated. Check {} for errors in building.'
.format(logpath))
if ionize:
shutil.move(os.path.join(outdir, 'structure.crd'),
os.path.join(outdir, 'structure.noions.crd'))
shutil.move(os.path.join(outdir, 'structure.prmtop'),
os.path.join(outdir, 'structure.noions.prmtop'))
totalcharge = np.sum(molbuilt.charge)
nwater = np.sum(molbuilt.atomselect('water and noh'))
anion, cation, anionatom, cationatom, nanion, ncation = ionizef(
totalcharge,
nwater,
saltconc=saltconc,
anion=saltanion,
cation=saltcation)
newmol = ionizePlace(mol, anion, cation, anionatom, cationatom,
nanion, ncation)
# Redo the whole build but now with ions included
return build(newmol,
ff=ff,
topo=topo,
param=param,
prefix=prefix,
outdir=outdir,
caps={},
ionize=False,
execute=execute,
saltconc=saltconc,
disulfide=disulfide,
tleap=tleap,
atomtypes=atomtypes,
offlibraries=offlibraries)
tmpbonds = molbuilt.bonds
molbuilt.bonds = [] # Removing the bonds to speed up writing
molbuilt.write(os.path.join(outdir, 'structure.pdb'))
molbuilt.bonds = tmpbonds # Restoring the bonds
return molbuilt
def build(mol,
topo=None,
param=None,
stream=None,
prefix='structure',
outdir='./build',
caps=None,
ionize=True,
saltconc=0,
saltanion=None,
saltcation=None,
disulfide=None,
patches=None,
noregen=None,
psfgen=None,
execute=True,
_clean=True):
""" Builds a system for CHARMM
Uses VMD and psfgen to build a system for CHARMM. Additionally it allows for ionization and adding of disulfide bridges.
Parameters
----------
mol : :class:`Molecule <htmd.molecule.molecule.Molecule>` object
The Molecule object containing the system
topo : list of str
A list of topology `rtf` files.
Use :func:`charmm.listFiles <htmd.builder.charmm.listFiles>` to get a list of available topology files.
Default: ['top/top_all36_prot.rtf', 'top/top_all36_lipid.rtf', 'top/top_water_ions.rtf']
param : list of str
A list of parameter `prm` files.
Use :func:`charmm.listFiles <htmd.builder.charmm.listFiles>` to get a list of available parameter files.
Default: ['par/par_all36_prot_mod.prm', 'par/par_all36_lipid.prm', 'par/par_water_ions.prm']
stream : list of str
A list of stream `str` files containing topologies and parameters.
Use :func:`charmm.listFiles <htmd.builder.charmm.listFiles>` to get a list of available stream files.
Default: ['str/prot/toppar_all36_prot_arg0.str']
prefix : str
The prefix for the generated pdb and psf files
outdir : str
The path to the output directory
Default: './build'
caps : dict
A dictionary with keys segids and values lists of strings describing the caps of that segment.
e.g. caps['P'] = ['first ACE', 'last CT3'] or caps['P'] = ['first none', 'last none'].
Default: will apply ACE and CT3 caps to proteins and none caps to the rest.
ionize : bool
Enable or disable ionization
saltconc : float
Salt concentration (in Molar) to add to the system after neutralization.
saltanion : {'CLA'}
The anion type. Please use only CHARMM ion atom names.
saltcation : {'SOD', 'MG', 'POT', 'CES', 'CAL', 'ZN2'}
The cation type. Please use only CHARMM ion atom names.
disulfide : list of pairs of atomselection strings
If None it will guess disulfide bonds. Otherwise provide a list pairs of atomselection strings for each pair of
residues forming the disulfide bridge.
patches : list of str
Any further patches the user wants to apply
noregen : list of str
A list of patches that must not be regenerated (angles and dihedrals)
Default: ['FHEM', 'PHEM', 'PLOH', 'PLO2', 'PLIG', 'PSUL']
psfgen : str
Path to psfgen executable used to build for CHARMM
execute : bool
Disable building. Will only write out the input script needed by psfgen. Does not include ionization.
Returns
-------
molbuilt : :class:`Molecule <htmd.molecule.molecule.Molecule>` object
The built system in a Molecule object
Example
-------
>>> from htmd.ui import *
>>> mol = Molecule("3PTB")
>>> mol.filter("not resname BEN")
>>> molbuilt = charmm.build(mol, outdir='/tmp/build', ionize=False) # doctest: +ELLIPSIS
Bond between A: [serial 185 resid 42 resname CYS chain A segid 0]
B: [serial 298 resid 58 resname CYS chain A segid 0]...
>>> # More complex example
>>> topos = ['top/top_all36_prot.rtf', './benzamidine.rtf', 'top/top_water_ions.rtf']
>>> params = ['par/par_all36_prot_mod.prm', './benzamidine.prm', 'par/par_water_ions.prm']
>>> disu = [['segid P and resid 157', 'segid P and resid 13'], ['segid K and resid 1', 'segid K and resid 25']]
>>> molbuilt = charmm.build(mol, topo=topos, param=params, outdir='/tmp/build', saltconc=0.15, disulfide=disu) # doctest: +SKIP
"""
mol = mol.copy()
_missingSegID(mol)
_checkMixedSegment(mol)
if psfgen is None:
psfgen = shutil.which('psfgen', mode=os.X_OK)
if not psfgen:
raise FileNotFoundError(
'Could not find psfgen executable, or no execute permissions are given. '
'Run `conda install psfgen`.')
if not os.path.isdir(outdir):
os.makedirs(outdir)
if _clean:
_cleanOutDir(outdir)
if topo is None:
topo = defaultTopo()
if param is None:
param = defaultParam()
if stream is None:
stream = defaultStream()
if caps is None:
caps = _defaultCaps(mol)
# patches that must _not_ be regenerated
if noregen is None:
noregen = ['FHEM', 'PHEM', 'PLOH', 'PLO2', 'PLIG', 'PSUL']
alltopo = topo.copy()
allparam = param.copy()
# Splitting the stream files and adding them to the list of parameter and topology files
charmmdir = path.join(home(), 'builder', 'charmmfiles')
for s in stream:
if s[0] != '.' and path.isfile(path.join(charmmdir, s)):
s = path.join(charmmdir, s)
outrtf, outprm = _prepareStream(s)
alltopo.append(outrtf)
allparam.append(outprm)
#_missingChain(mol)
#_checkProteinGaps(mol)
if patches is None:
patches = []
if isinstance(patches, str):
patches = [patches]
allpatches = []
allpatches += patches
# Find protonated residues and add patches for them
allpatches += _protonationPatches(mol)
f = open(path.join(outdir, 'build.vmd'), 'w')
f.write('# psfgen file generated by charmm.build\n')
f.write('package require psfgen;\n')
f.write('psfcontext reset;\n\n')
# Copying and printing out the topologies
if not path.exists(path.join(outdir, 'topologies')):
os.makedirs(path.join(outdir, 'topologies'))
for i in range(len(alltopo)):
if alltopo[i][0] != '.' and path.isfile(
path.join(charmmdir, alltopo[i])):
alltopo[i] = path.join(charmmdir, alltopo[i])
localname = '{}.'.format(i) + path.basename(alltopo[i])
shutil.copy(alltopo[i], path.join(outdir, 'topologies', localname))
f.write('topology ' + path.join('topologies', localname) + '\n')
f.write('\n')
_printAliases(f)
# Printing out segments
if not path.exists(path.join(outdir, 'segments')):
os.makedirs(path.join(outdir, 'segments'))
logger.info('Writing out segments.')
segments = _getSegments(mol)
wateratoms = mol.atomselect('water')
for seg in segments:
pdbname = 'segment' + seg + '.pdb'
segatoms = mol.segid == seg
mol.write(path.join(outdir, 'segments', pdbname), sel=segatoms)
segwater = wateratoms & segatoms
f.write('segment ' + seg + ' {\n')
if np.all(segatoms ==
segwater): # If segment only contains waters, set: auto none
f.write('\tauto none\n')
f.write('\tpdb ' + path.join('segments', pdbname) + '\n')
if caps is not None and seg in caps:
for c in caps[seg]:
f.write('\t' + c + '\n')
f.write('}\n')
f.write('coordpdb ' + path.join('segments', pdbname) + ' ' + seg +
'\n\n')
# Printing out patches for the disulfide bridges
# TODO: Remove this once we deprecate the class
from htmd.builder.builder import DisulfideBridge
from htmd.molecule.molecule import UniqueResidueID
if disulfide is not None and len(disulfide) != 0 and isinstance(
disulfide[0], DisulfideBridge):
newdisu = []
for d in disulfide:
r1 = UniqueResidueID.fromMolecule(
mol, 'resid {} and segname {}'.format(d.resid1, d.segid1))
r2 = UniqueResidueID.fromMolecule(
mol, 'resid {} and segname {}'.format(d.resid2, d.segid2))
newdisu.append([r1, r2])
disulfide = newdisu
# TODO: Remove up to here ----------------------
if disulfide is not None and len(disulfide) != 0 and isinstance(
disulfide[0][0], str):
disulfide = convertDisulfide(mol, disulfide)
if disulfide is None:
disulfide = detectDisulfideBonds(mol)
if len(disulfide) != 0:
for d in disulfide:
str0 = '{}:{}{}'.format(d[0].segid, d[0].resid, d[0].insertion)
str1 = '{}:{}{}'.format(d[1].segid, d[1].resid, d[1].insertion)
f.write('patch DISU {} {}\n'.format(str0, str1))
f.write('\n')
noregenpatches = [p for p in allpatches if p.split()[1] in noregen]
regenpatches = [p for p in allpatches if p.split()[1] not in noregen]
# Printing regenerable patches
if len(regenpatches) != 0:
for p in regenpatches:
f.write(p + '\n')
f.write('\n')
# Regenerate angles and dihedrals
f.write('regenerate angles dihedrals\n')
f.write('\n')
# Printing non-regenerable patches
if len(noregenpatches) != 0:
for p in noregenpatches:
f.write(p + '\n')
f.write('\n')
f.write('guesscoord\n')
f.write('writepsf ' + prefix + '.psf\n')
f.write('writepdb ' + prefix + '.pdb\n')
#f.write('quit\n')
f.close()
if allparam is not None:
combine(allparam, path.join(outdir, 'parameters'))
molbuilt = None
if execute:
logpath = os.path.abspath('{}/log.txt'.format(outdir))
logger.info('Starting the build.')
currdir = os.getcwd()
os.chdir(outdir)
f = open(logpath, 'w')
#call([vmd, '-dispdev', 'text', '-e', './build.vmd'], stdout=f)
call([psfgen, './build.vmd'], stdout=f)
f.close()
errors = _logParser(logpath)
os.chdir(currdir)
if errors:
raise BuildError(errors + [
'Check {} for further information on errors in building.'.
format(logpath)
])
logger.info('Finished building.')
if path.isfile(path.join(outdir, 'structure.pdb')) and path.isfile(
path.join(outdir, 'structure.psf')):
molbuilt = Molecule(path.join(outdir, 'structure.pdb'))
molbuilt.read(path.join(outdir, 'structure.psf'))
else:
raise BuildError(
'No structure pdb/psf file was generated. Check {} for errors in building.'
.format(logpath))
if ionize:
os.makedirs(path.join(outdir, 'pre-ionize'))
data = glob(path.join(outdir, '*'))
for f in data:
shutil.move(f, path.join(outdir, 'pre-ionize'))
totalcharge = np.sum(molbuilt.charge)
nwater = np.sum(molbuilt.atomselect('water and noh'))
anion, cation, anionatom, cationatom, nanion, ncation = ionizef(
totalcharge,
nwater,
saltconc=saltconc,
anion=saltanion,
cation=saltcation)
newmol = ionizePlace(mol, anion, cation, anionatom, cationatom,
nanion, ncation)
# Redo the whole build but now with ions included
return build(newmol,
topo=alltopo,
param=allparam,
stream=[],
prefix=prefix,
outdir=outdir,
ionize=False,
caps=caps,
execute=execute,
saltconc=saltconc,
disulfide=disulfide,
patches=patches,
noregen=noregen,
psfgen=psfgen,
_clean=False)
_checkFailedAtoms(molbuilt)
_recoverProtonations(molbuilt)
return molbuilt
def build(mol, ff=None, topo=None, param=None, prefix='structure', outdir='./build', caps=None, ionize=True, saltconc=0,
saltanion=None, saltcation=None, disulfide=None, tleap=None, execute=True, atomtypes=None,
offlibraries=None, gbsa=False, igb=2):
""" Builds a system for AMBER
Uses tleap to build a system for AMBER. Additionally it allows the user to ionize and add disulfide bridges.
Parameters
----------
mol : :class:`Molecule <htmd.molecule.molecule.Molecule>` object
The Molecule object containing the system
ff : list of str
A list of leaprc forcefield files.
Use :func:`amber.listFiles <htmd.builder.amber.listFiles>` to get a list of available forcefield files.
Default: :func:`amber.defaultFf <htmd.builder.amber.defaultFf>`
topo : list of str
A list of topology `prepi/prep/in` files.
Use :func:`amber.listFiles <htmd.builder.amber.listFiles>` to get a list of available topology files.
Default: :func:`amber.defaultTopo <htmd.builder.amber.defaultTopo>`
param : list of str
A list of parameter `frcmod` files.
Use :func:`amber.listFiles <htmd.builder.amber.listFiles>` to get a list of available parameter files.
Default: :func:`amber.defaultParam <htmd.builder.amber.defaultParam>`
prefix : str
The prefix for the generated pdb and psf files
outdir : str
The path to the output directory
Default: './build'
caps : dict
A dictionary with keys segids and values lists of strings describing the caps for a particular protein segment.
e.g. caps['P'] = ['ACE', 'NME'] or caps['P'] = ['none', 'none']. Default: will apply ACE and NME caps to every
protein segment.
ionize : bool
Enable or disable ionization
saltconc : float
Salt concentration to add to the system after neutralization.
saltanion : {'Cl-'}
The anion type. Please use only AMBER ion atom names.
saltcation : {'Na+', 'K+', 'Cs+'}
The cation type. Please use only AMBER ion atom names.
disulfide : list of pairs of atomselection strings
If None it will guess disulfide bonds. Otherwise provide a list pairs of atomselection strings for each pair of
residues forming the disulfide bridge.
tleap : str
Path to tleap executable used to build the system for AMBER
execute : bool
Disable building. Will only write out the input script needed by tleap. Does not include ionization.
atomtypes : list of triplets
Custom atom types defined by the user as ('type', 'element', 'hybrid') triplets
e.g. (('C1', 'C', 'sp2'), ('CI', 'C', 'sp3')). Check `addAtomTypes` in AmberTools docs.
offlibraries : str or list
A path or a list of paths to OFF library files. Check `loadOFF` in AmberTools docs.
gbsa : bool
Modify radii for GBSA implicit water model
igb : int
GB model. Select: 1 for mbondi, 2 and 5 for mbondi2, 7 for bondi and 8 for mbondi3.
Check section 4. The Generalized Born/Surface Area Model of the AMBER manual.
Returns
-------
molbuilt : :class:`Molecule <htmd.molecule.molecule.Molecule>` object
The built system in a Molecule object
Example
-------
>>> from htmd.ui import * # doctest: +SKIP
>>> mol = Molecule("3PTB")
>>> molbuilt = amber.build(mol, outdir='/tmp/build') # doctest: +SKIP
>>> # More complex example
>>> disu = [['segid P and resid 157', 'segid P and resid 13'], ['segid K and resid 1', 'segid K and resid 25']]
>>> molbuilt = amber.build(mol, outdir='/tmp/build', saltconc=0.15, disulfide=disu) # doctest: +SKIP
"""
# Remove pdb protein bonds as they can be regenerated by tleap. Keep non-protein bonds i.e. for ligands
mol = mol.copy()
_removeProteinBonds(mol)
if tleap is None:
tleap = _findTleap()
else:
if shutil.which(tleap) is None:
raise NameError('Could not find executable: `{}` in the PATH. Cannot build for AMBER.'.format(tleap))
if not os.path.isdir(outdir):
os.makedirs(outdir)
_cleanOutDir(outdir)
if ff is None:
ff = defaultFf()
if topo is None:
topo = defaultTopo()
if param is None:
param = defaultParam()
if caps is None:
caps = _defaultProteinCaps(mol)
_missingSegID(mol)
_checkMixedSegment(mol)
mol = _charmmLipid2Amber(mol)
_applyProteinCaps(mol, caps)
f = open(os.path.join(outdir, 'tleap.in'), 'w')
f.write('# tleap file generated by amber.build\n')
# Printing out the forcefields
if isinstance(ff, str):
ff = [ff]
for i, force in enumerate(ff):
if not os.path.isfile(force):
force = _locateFile(force, 'ff', tleap)
if force is None:
continue
newname = 'ff{}_{}'.format(i, os.path.basename(force))
shutil.copy(force, os.path.join(outdir, newname))
f.write('source {}\n'.format(newname))
f.write('\n')
if gbsa:
gbmodels = {1: 'mbondi', 2: 'mbondi2', 5: 'mbondi2', 7: 'bondi', 8: 'mbondi3'}
f.write('set default PBradii {}\n\n'.format(gbmodels[igb]))
# Adding custom atom types
if atomtypes is not None:
atomtypes = ensurelist(tocheck=atomtypes[0], tomod=atomtypes)
f.write('addAtomTypes {\n')
for at in atomtypes:
if len(at) != 3:
raise RuntimeError('Atom type definitions have to be triplets. Check the AMBER documentation.')
f.write(' {{ "{}" "{}" "{}" }}\n'.format(at[0], at[1], at[2]))
f.write('}\n\n')
# Loading OFF libraries
if offlibraries is not None:
offlibraries = ensurelist(offlibraries)
for off in offlibraries:
if not os.path.isfile(off):
raise RuntimeError('Could not find off-library in location {}'.format(off))
newname = 'offlib{}_{}'.format(i, os.path.basename(off))
shutil.copy(off, os.path.join(outdir, newname))
f.write('loadoff {}\n'.format(newname))
# Loading frcmod parameters
f.write('# Loading parameter files\n')
for i, p in enumerate(param):
if not os.path.isfile(p):
p = _locateFile(p, 'param', tleap)
if p is None:
continue
newname = 'param{}_{}'.format(i, os.path.basename(p))
shutil.copy(p, os.path.join(outdir, newname))
f.write('loadamberparams {}\n'.format(newname))
f.write('\n')
# Loading prepi topologies
f.write('# Loading prepi topologies\n')
for i, t in enumerate(topo):
if not os.path.isfile(t):
t = _locateFile(t, 'topo', tleap)
if t is None:
continue
newname = 'topo{}_{}'.format(i, os.path.basename(t))
shutil.copy(t, os.path.join(outdir, newname))
f.write('loadamberprep {}\n'.format(newname))
f.write('\n')
f.write('# Loading the system\n')
f.write('mol = loadpdb input.pdb\n\n')
if np.sum(mol.atomtype != '') != 0:
logger.debug('Writing mol2 files for input to tleap.')
segs = np.unique(mol.segid[mol.atomtype != ''])
combstr = 'mol = combine {mol'
for s in segs:
name = 'segment{}'.format(s)
mol2name = os.path.join(outdir, '{}.mol2'.format(name))
mol.write(mol2name, (mol.atomtype != '') & (mol.segid == s))
if not os.path.isfile(mol2name):
raise NameError('Could not write a mol2 file out of the given Molecule.')
f.write('# Loading the rest of the system\n')
f.write('{} = loadmol2 {}.mol2\n\n'.format(name, name))
combstr += ' {}'.format(name)
combstr += '}\n\n'
f.write(combstr)
# Write patches for disulfide bonds (only after ionizing)
if not ionize:
# TODO: Remove this once we deprecate the class
from htmd.builder.builder import DisulfideBridge
from htmd.molecule.molecule import UniqueResidueID
if disulfide is not None and len(disulfide) != 0 and isinstance(disulfide[0], DisulfideBridge):
newdisu = []
for d in disulfide:
r1 = UniqueResidueID.fromMolecule(mol, 'resid {} and segname {}'.format(d.resid1, d.segid1))
r2 = UniqueResidueID.fromMolecule(mol, 'resid {} and segname {}'.format(d.resid2, d.segid2))
newdisu.append([r1, r2])
disulfide = newdisu
# TODO: Remove up to here ----------------------
if disulfide is not None and len(disulfide) != 0 and isinstance(disulfide[0][0], str):
disulfide = convertDisulfide(mol, disulfide)
if disulfide is None:
logger.info('Detecting disulfide bonds.')
disulfide = detectDisulfideBonds(mol)
# Fix structure to match the disulfide patching
if len(disulfide) != 0:
torem = np.zeros(mol.numAtoms, dtype=bool)
f.write('# Adding disulfide bonds\n')
for d in disulfide:
# Rename the residues to CYX if there is a disulfide bond
atoms1 = d[0].selectAtoms(mol, indexes=False)
atoms2 = d[1].selectAtoms(mol, indexes=False)
mol.resname[atoms1] = 'CYX'
mol.resname[atoms2] = 'CYX'
# Remove (eventual) HG hydrogens on these CYS (from proteinPrepare)
torem |= (atoms1 & (mol.name == 'HG')) | (atoms2 & (mol.name == 'HG'))
# Convert to stupid amber residue numbering
uqseqid = sequenceID((mol.resid, mol.insertion, mol.segid)) + mol.resid[0]
uqres1 = int(np.unique(uqseqid[atoms1]))
uqres2 = int(np.unique(uqseqid[atoms2]))
f.write('bond mol.{}.SG mol.{}.SG\n'.format(uqres1, uqres2))
f.write('\n')
mol.remove(torem, _logger=False)
f.write('# Writing out the results\n')
f.write('saveamberparm mol ' + prefix + '.prmtop ' + prefix + '.crd\n')
f.write('quit')
f.close()
# Printing and loading the PDB file. AMBER can work with a single PDB file if the segments are separate by TER
logger.debug('Writing PDB file for input to tleap.')
pdbname = os.path.join(outdir, 'input.pdb')
# mol2 files have atomtype, here we only write parts not coming from mol2
# We need to write the input.pdb at the end since we modify the resname for disulfide bridges in mol
mol.write(pdbname, mol.atomtype == '')
if not os.path.isfile(pdbname):
raise NameError('Could not write a PDB file out of the given Molecule.')
molbuilt = None
if execute:
# Source paths of extra dirs (our dirs, not amber default)
htmdamberdir = os.path.abspath(os.path.join(home(), 'builder', 'amberfiles'))
sourcepaths = [htmdamberdir]
sourcepaths += [os.path.join(htmdamberdir, os.path.dirname(f))
for f in ff if os.path.isfile(os.path.join(htmdamberdir, f))]
extrasource = []
for p in sourcepaths:
extrasource.append('-I')
extrasource.append('{}'.format(p))
logpath = os.path.abspath(os.path.join(outdir, 'log.txt'))
logger.info('Starting the build.')
currdir = os.getcwd()
os.chdir(outdir)
f = open(logpath, 'w')
try:
cmd = [tleap, '-f', './tleap.in']
cmd[1:1] = extrasource
call(cmd, stdout=f)
except:
raise NameError('tleap failed at execution')
f.close()
errors = _logParser(logpath)
os.chdir(currdir)
if errors:
raise BuildError(errors + ['Check {} for further information on errors in building.'.format(logpath)])
logger.info('Finished building.')
if os.path.exists(os.path.join(outdir, 'structure.crd')) and \
os.path.getsize(os.path.join(outdir, 'structure.crd')) != 0 and \
os.path.getsize(os.path.join(outdir, 'structure.prmtop')) != 0:
molbuilt = Molecule(os.path.join(outdir, 'structure.prmtop'))
molbuilt.read(os.path.join(outdir, 'structure.crd'))
else:
raise BuildError('No structure pdb/prmtop file was generated. Check {} for errors in building.'.format(logpath))
if ionize:
shutil.move(os.path.join(outdir, 'structure.crd'), os.path.join(outdir, 'structure.noions.crd'))
shutil.move(os.path.join(outdir, 'structure.prmtop'), os.path.join(outdir, 'structure.noions.prmtop'))
totalcharge = np.sum(molbuilt.charge)
nwater = np.sum(molbuilt.atomselect('water and noh'))
anion, cation, anionatom, cationatom, nanion, ncation = ionizef(totalcharge, nwater, saltconc=saltconc,
anion=saltanion, cation=saltcation)
newmol = ionizePlace(mol, anion, cation, anionatom, cationatom, nanion, ncation)
# Redo the whole build but now with ions included
return build(newmol, ff=ff, topo=topo, param=param, prefix=prefix, outdir=outdir, caps={}, ionize=False,
execute=execute, saltconc=saltconc, disulfide=disulfide, tleap=tleap, atomtypes=atomtypes,
offlibraries=offlibraries)
tmpbonds = molbuilt.bonds
molbuilt.bonds = [] # Removing the bonds to speed up writing
molbuilt.write(os.path.join(outdir, 'structure.pdb'))
molbuilt.bonds = tmpbonds # Restoring the bonds
return molbuilt
def build(mol, topo=None, param=None, stream=None, prefix='structure', outdir='./build', caps=None, ionize=True, saltconc=0,
saltanion=None, saltcation=None, disulfide=None, patches=None, noregen=None, psfgen=None, execute=True, _clean=True):
""" Builds a system for CHARMM
Uses VMD and psfgen to build a system for CHARMM. Additionally it allows for ionization and adding of disulfide bridges.
Parameters
----------
mol : :class:`Molecule <htmd.molecule.molecule.Molecule>` object
The Molecule object containing the system
topo : list of str
A list of topology `rtf` files.
Use :func:`charmm.listFiles <htmd.builder.charmm.listFiles>` to get a list of available topology files.
Default: ['top/top_all36_prot.rtf', 'top/top_all36_lipid.rtf', 'top/top_water_ions.rtf']
param : list of str
A list of parameter `prm` files.
Use :func:`charmm.listFiles <htmd.builder.charmm.listFiles>` to get a list of available parameter files.
Default: ['par/par_all36_prot_mod.prm', 'par/par_all36_lipid.prm', 'par/par_water_ions.prm']
stream : list of str
A list of stream `str` files containing topologies and parameters.
Use :func:`charmm.listFiles <htmd.builder.charmm.listFiles>` to get a list of available stream files.
Default: ['str/prot/toppar_all36_prot_arg0.str']
prefix : str
The prefix for the generated pdb and psf files
outdir : str
The path to the output directory
Default: './build'
caps : dict
A dictionary with keys segids and values lists of strings describing the caps of that segment.
e.g. caps['P'] = ['first ACE', 'last CT3'] or caps['P'] = ['first none', 'last none'].
Default: will apply ACE and CT3 caps to proteins and none caps to the rest.
ionize : bool
Enable or disable ionization
saltconc : float
Salt concentration (in Molar) to add to the system after neutralization.
saltanion : {'CLA'}
The anion type. Please use only CHARMM ion atom names.
saltcation : {'SOD', 'MG', 'POT', 'CES', 'CAL', 'ZN2'}
The cation type. Please use only CHARMM ion atom names.
disulfide : list of pairs of atomselection strings
If None it will guess disulfide bonds. Otherwise provide a list pairs of atomselection strings for each pair of
residues forming the disulfide bridge.
patches : list of str
Any further patches the user wants to apply
noregen : list of str
A list of patches that must not be regenerated (angles and dihedrals)
Default: ['FHEM', 'PHEM', 'PLOH', 'PLO2', 'PLIG', 'PSUL']
psfgen : str
Path to psfgen executable used to build for CHARMM
execute : bool
Disable building. Will only write out the input script needed by psfgen. Does not include ionization.
Returns
-------
molbuilt : :class:`Molecule <htmd.molecule.molecule.Molecule>` object
The built system in a Molecule object
Example
-------
>>> from htmd.ui import *
>>> mol = Molecule("3PTB")
>>> mol.filter("not resname BEN")
>>> molbuilt = charmm.build(mol, outdir='/tmp/build', ionize=False) # doctest: +ELLIPSIS
Bond between A: [serial 185 resid 42 resname CYS chain A segid 0]
B: [serial 298 resid 58 resname CYS chain A segid 0]...
>>> # More complex example
>>> topos = ['top/top_all36_prot.rtf', './benzamidine.rtf', 'top/top_water_ions.rtf']
>>> params = ['par/par_all36_prot_mod.prm', './benzamidine.prm', 'par/par_water_ions.prm']
>>> disu = [['segid P and resid 157', 'segid P and resid 13'], ['segid K and resid 1', 'segid K and resid 25']]
>>> molbuilt = charmm.build(mol, topo=topos, param=params, outdir='/tmp/build', saltconc=0.15, disulfide=disu) # doctest: +SKIP
"""
mol = mol.copy()
_missingSegID(mol)
_checkMixedSegment(mol)
if psfgen is None:
psfgen = shutil.which('psfgen', mode=os.X_OK)
if not psfgen:
raise FileNotFoundError('Could not find psfgen executable, or no execute permissions are given. '
'Run `conda install psfgen`.')
if not os.path.isdir(outdir):
os.makedirs(outdir)
if _clean:
_cleanOutDir(outdir)
if topo is None:
topo = defaultTopo()
if param is None:
param = defaultParam()
if stream is None:
stream = defaultStream()
if caps is None:
caps = _defaultCaps(mol)
# patches that must _not_ be regenerated
if noregen is None:
noregen = ['FHEM', 'PHEM', 'PLOH', 'PLO2', 'PLIG', 'PSUL']
alltopo = topo.copy()
allparam = param.copy()
# Splitting the stream files and adding them to the list of parameter and topology files
charmmdir = path.join(home(), 'builder', 'charmmfiles')
for s in stream:
if s[0] != '.' and path.isfile(path.join(charmmdir, s)):
s = path.join(charmmdir, s)
outrtf, outprm = _prepareStream(s)
alltopo.append(outrtf)
allparam.append(outprm)
#_missingChain(mol)
#_checkProteinGaps(mol)
if patches is None:
patches = []
if isinstance(patches, str):
patches = [patches]
allpatches = []
allpatches += patches
# Find protonated residues and add patches for them
allpatches += _protonationPatches(mol)
f = open(path.join(outdir, 'build.vmd'), 'w')
f.write('# psfgen file generated by charmm.build\n')
f.write('package require psfgen;\n')
f.write('psfcontext reset;\n\n')
# Copying and printing out the topologies
if not path.exists(path.join(outdir, 'topologies')):
os.makedirs(path.join(outdir, 'topologies'))
for i in range(len(alltopo)):
if alltopo[i][0] != '.' and path.isfile(path.join(charmmdir, alltopo[i])):
alltopo[i] = path.join(charmmdir, alltopo[i])
localname = '{}.'.format(i) + path.basename(alltopo[i])
shutil.copy(alltopo[i], path.join(outdir, 'topologies', localname))
f.write('topology ' + path.join('topologies', localname) + '\n')
f.write('\n')
_printAliases(f)
# Printing out segments
if not path.exists(path.join(outdir, 'segments')):
os.makedirs(path.join(outdir, 'segments'))
logger.info('Writing out segments.')
segments = _getSegments(mol)
wateratoms = mol.atomselect('water')
for seg in segments:
pdbname = 'segment' + seg + '.pdb'
segatoms = mol.segid == seg
mol.write(path.join(outdir, 'segments', pdbname), sel=segatoms)
segwater = wateratoms & segatoms
f.write('segment ' + seg + ' {\n')
if np.all(segatoms == segwater): # If segment only contains waters, set: auto none
f.write('\tauto none\n')
f.write('\tpdb ' + path.join('segments', pdbname) + '\n')
if caps is not None and seg in caps:
for c in caps[seg]:
f.write('\t' + c + '\n')
f.write('}\n')
f.write('coordpdb ' + path.join('segments', pdbname) + ' ' + seg + '\n\n')
# Printing out patches for the disulfide bridges
# TODO: Remove this once we deprecate the class
from htmd.builder.builder import DisulfideBridge
from htmd.molecule.molecule import UniqueResidueID
if disulfide is not None and len(disulfide) != 0 and isinstance(disulfide[0], DisulfideBridge):
newdisu = []
for d in disulfide:
r1 = UniqueResidueID.fromMolecule(mol, 'resid {} and segname {}'.format(d.resid1, d.segid1))
r2 = UniqueResidueID.fromMolecule(mol, 'resid {} and segname {}'.format(d.resid2, d.segid2))
newdisu.append([r1, r2])
disulfide = newdisu
# TODO: Remove up to here ----------------------
if disulfide is not None and len(disulfide) != 0 and isinstance(disulfide[0][0], str):
disulfide = convertDisulfide(mol, disulfide)
if disulfide is None:
disulfide = detectDisulfideBonds(mol)
if len(disulfide) != 0:
for d in disulfide:
str0 = '{}:{}{}'.format(d[0].segid, d[0].resid, d[0].insertion)
str1 = '{}:{}{}'.format(d[1].segid, d[1].resid, d[1].insertion)
f.write('patch DISU {} {}\n'.format(str0, str1))
f.write('\n')
noregenpatches = [p for p in allpatches if p.split()[1] in noregen]
regenpatches = [p for p in allpatches if p.split()[1] not in noregen]
# Printing regenerable patches
if len(regenpatches) != 0:
for p in regenpatches:
f.write(p + '\n')
f.write('\n')
# Regenerate angles and dihedrals
f.write('regenerate angles dihedrals\n')
f.write('\n')
# Printing non-regenerable patches
if len(noregenpatches) != 0:
for p in noregenpatches:
f.write(p + '\n')
f.write('\n')
f.write('guesscoord\n')
f.write('writepsf ' + prefix + '.psf\n')
f.write('writepdb ' + prefix + '.pdb\n')
#f.write('quit\n')
f.close()
if allparam is not None:
combine(allparam, path.join(outdir, 'parameters'))
molbuilt = None
if execute:
logpath = os.path.abspath('{}/log.txt'.format(outdir))
logger.info('Starting the build.')
currdir = os.getcwd()
os.chdir(outdir)
f = open(logpath, 'w')
#call([vmd, '-dispdev', 'text', '-e', './build.vmd'], stdout=f)
call([psfgen, './build.vmd'], stdout=f)
f.close()
errors = _logParser(logpath)
os.chdir(currdir)
if errors:
raise BuildError(errors + ['Check {} for further information on errors in building.'.format(logpath)])
logger.info('Finished building.')
if path.isfile(path.join(outdir, 'structure.pdb')) and path.isfile(path.join(outdir, 'structure.psf')):
molbuilt = Molecule(path.join(outdir, 'structure.pdb'))
molbuilt.read(path.join(outdir, 'structure.psf'))
else:
raise BuildError('No structure pdb/psf file was generated. Check {} for errors in building.'.format(logpath))
if ionize:
os.makedirs(path.join(outdir, 'pre-ionize'))
data = glob(path.join(outdir, '*'))
for f in data:
shutil.move(f, path.join(outdir, 'pre-ionize'))
totalcharge = np.sum(molbuilt.charge)
nwater = np.sum(molbuilt.atomselect('water and noh'))
anion, cation, anionatom, cationatom, nanion, ncation = ionizef(totalcharge, nwater, saltconc=saltconc,
anion=saltanion, cation=saltcation)
newmol = ionizePlace(mol, anion, cation, anionatom, cationatom, nanion, ncation)
# Redo the whole build but now with ions included
return build(newmol, topo=alltopo, param=allparam, stream=[], prefix=prefix, outdir=outdir, ionize=False,
caps=caps, execute=execute, saltconc=saltconc, disulfide=disulfide, patches=patches,
noregen=noregen, psfgen=psfgen, _clean=False)
_checkFailedAtoms(molbuilt)
_recoverProtonations(molbuilt)
return molbuilt
def build(
mol,
ff=None,
topo=None,
param=None,
prefix="structure",
outdir="./build",
caps=None,
ionize=True,
saltconc=0,
saltanion=None,
saltcation=None,
disulfide=None,
teleap=None,
teleapimports=None,
execute=True,
atomtypes=None,
offlibraries=None,
gbsa=False,
igb=2,
):
"""Builds a system for AMBER
Uses tleap to build a system for AMBER. Additionally it allows the user to ionize and add disulfide bridges.
Parameters
----------
mol : :class:`Molecule <moleculekit.molecule.Molecule>` object
The Molecule object containing the system
ff : list of str
A list of leaprc forcefield files.
Use :func:`amber.listFiles <htmd.builder.amber.listFiles>` to get a list of available forcefield files.
Default: :func:`amber.defaultFf <htmd.builder.amber.defaultFf>`
topo : list of str
A list of topology `prepi/prep/in` files.
Use :func:`amber.listFiles <htmd.builder.amber.listFiles>` to get a list of available topology files.
Default: :func:`amber.defaultTopo <htmd.builder.amber.defaultTopo>`
param : list of str
A list of parameter `frcmod` files.
Use :func:`amber.listFiles <htmd.builder.amber.listFiles>` to get a list of available parameter files.
Default: :func:`amber.defaultParam <htmd.builder.amber.defaultParam>`
prefix : str
The prefix for the generated pdb and psf files
outdir : str
The path to the output directory
Default: './build'
caps : dict
A dictionary with keys segids and values lists of strings describing the caps for a particular protein segment.
e.g. caps['P'] = ['ACE', 'NME'] or caps['P'] = ['none', 'none']. Default: will apply ACE and NME caps to every
protein segment.
ionize : bool
Enable or disable ionization
saltconc : float
Salt concentration to add to the system after neutralization.
saltanion : {'Cl-'}
The anion type. Please use only AMBER ion atom names.
saltcation : {'Na+', 'K+', 'Cs+'}
The cation type. Please use only AMBER ion atom names.
disulfide : list of pairs of atomselection strings
If None it will guess disulfide bonds. Otherwise provide a list pairs of atomselection strings for each pair of
residues forming the disulfide bridge.
teleap : str
Path to teLeap executable used to build the system for AMBER
teleapimports : list
A list of paths to pass to teLeap '-I' flag, i.e. directories to be searched
Default: determined from :func:`amber.defaultAmberHome <htmd.builder.amber.defaultAmberHome>` and
:func:`amber.htmdAmberHome <htmd.builder.amber.htmdAmberHome>`
execute : bool
Disable building. Will only write out the input script needed by tleap. Does not include ionization.
atomtypes : list of triplets
Custom atom types defined by the user as ('type', 'element', 'hybrid') triplets
e.g. (('C1', 'C', 'sp2'), ('CI', 'C', 'sp3')). Check `addAtomTypes` in AmberTools docs.
offlibraries : str or list
A path or a list of paths to OFF library files. Check `loadOFF` in AmberTools docs.
gbsa : bool
Modify radii for GBSA implicit water model
igb : int
GB model. Select: 1 for mbondi, 2 and 5 for mbondi2, 7 for bondi and 8 for mbondi3.
Check section 4. The Generalized Born/Surface Area Model of the AMBER manual.
Returns
-------
molbuilt : :class:`Molecule <moleculekit.molecule.Molecule>` object
The built system in a Molecule object
Example
-------
>>> from htmd.ui import * # doctest: +SKIP
>>> mol = Molecule("3PTB")
>>> molbuilt = amber.build(mol, outdir='/tmp/build') # doctest: +SKIP
>>> # More complex example
>>> disu = [['segid P and resid 157', 'segid P and resid 13'], ['segid K and resid 1', 'segid K and resid 25']]
>>> molbuilt = amber.build(mol, outdir='/tmp/build', saltconc=0.15, disulfide=disu) # doctest: +SKIP
"""
# Remove pdb protein bonds as they can be regenerated by tleap. Keep non-protein bonds i.e. for ligands
mol = mol.copy()
_removeProteinBonds(mol)
if teleap is None:
teleap = _findTeLeap()
else:
if shutil.which(teleap) is None:
raise NameError(
f"Could not find executable: `{teleap}` in the PATH. Cannot build for AMBER. Please install it with `conda install ambermini -c acellera`"
)
if not os.path.isdir(outdir):
os.makedirs(outdir)
_cleanOutDir(outdir)
if ff is None:
ff = defaultFf()
if topo is None:
topo = defaultTopo()
if param is None:
param = defaultParam()
if caps is None:
caps = _defaultProteinCaps(mol)
_missingSegID(mol)
_checkMixedSegment(mol)
mol = _charmmLipid2Amber(mol)
_applyProteinCaps(mol, caps)
f = open(os.path.join(outdir, "tleap.in"), "w")
f.write("# tleap file generated by amber.build\n")
# Printing out the forcefields
for i, force in enumerate(ensurelist(ff)):
if not os.path.isfile(force):
force = _locateFile(force, "ff", teleap)
if force is None:
continue
newname = f"ff{i}_{os.path.basename(force)}"
shutil.copy(force, os.path.join(outdir, newname))
f.write(f"source {newname}\n")
f.write("\n")
if gbsa:
gbmodels = {
1: "mbondi",
2: "mbondi2",
5: "mbondi2",
7: "bondi",
8: "mbondi3"
}
f.write(f"set default PBradii {gbmodels[igb]}\n\n")
# Adding custom atom types
if atomtypes is not None:
atomtypes = ensurelist(tocheck=atomtypes[0], tomod=atomtypes)
f.write("addAtomTypes {\n")
for at in atomtypes:
if len(at) != 3:
raise RuntimeError(
"Atom type definitions have to be triplets. Check the AMBER documentation."
)
f.write(f' {{ "{at[0]}" "{at[1]}" "{at[2]}" }}\n')
f.write("}\n\n")
# Loading OFF libraries
if offlibraries is not None:
offlibraries = ensurelist(offlibraries)
for i, off in enumerate(offlibraries):
if not os.path.isfile(off):
raise RuntimeError(
f"Could not find off-library in location {off}")
newname = f"offlib{i}_{os.path.basename(off)}"
shutil.copy(off, os.path.join(outdir, newname))
f.write(f"loadoff {newname}\n")
# Loading frcmod parameters
f.write("# Loading parameter files\n")
for i, p in enumerate(param):
if not os.path.isfile(p):
p = _locateFile(p, "param", teleap)
if p is None:
continue
newname = f"param{i}_{os.path.basename(p)}"
shutil.copy(p, os.path.join(outdir, newname))
f.write(f"loadamberparams {newname}\n")
f.write("\n")
# Loading prepi topologies
f.write("# Loading prepi topologies\n")
for i, t in enumerate(topo):
if not os.path.isfile(t):
t = _locateFile(t, "topo", teleap)
if t is None:
continue
newname = f"topo{i}_{os.path.basename(t)}"
shutil.copy(t, os.path.join(outdir, newname))
f.write(f"loadamberprep {newname}\n")
f.write("\n")
f.write("# Loading the system\n")
f.write("mol = loadpdb input.pdb\n\n")
if np.sum(mol.atomtype != "") != 0:
f.write("# Loading the ligands\n")
segs = np.unique(mol.segid[mol.atomtype != ""])
# teLeap crashes if you try to combine too many molecules in a single command so we will do them by 10s
for k in range(0, len(segs), 10):
segments_string = ""
for seg in segs[k:min(k + 10, len(segs))]:
name = f"segment{seg}"
segments_string += f" {name}"
mol2name = os.path.join(outdir, f"{name}.mol2")
mol.write(mol2name, (mol.atomtype != "") & (mol.segid == seg))
if not os.path.isfile(mol2name):
raise NameError("Failed writing ligand mol2 file.")
f.write(f"{name} = loadmol2 {name}.mol2\n")
f.write(f"mol = combine {{mol{segments_string}}}\n\n")
# Write patches for disulfide bonds (only after ionizing)
if not ionize:
# TODO: Remove this once we deprecate the class
from htmd.builder.builder import DisulfideBridge
from moleculekit.molecule import UniqueResidueID
if (disulfide is not None and len(disulfide) != 0
and isinstance(disulfide[0], DisulfideBridge)):
newdisu = []
for d in disulfide:
r1 = UniqueResidueID.fromMolecule(
mol, f"resid {d.resid1} and segname {d.segid1}")
r2 = UniqueResidueID.fromMolecule(
mol, f"resid {d.resid2} and segname {d.segid2}")
newdisu.append([r1, r2])
disulfide = newdisu
# TODO: Remove up to here ----------------------
if (disulfide is not None and len(disulfide) != 0
and isinstance(disulfide[0][0], str)):
disulfide = convertDisulfide(mol, disulfide)
if disulfide is None:
logger.info("Detecting disulfide bonds.")
disulfide = detectDisulfideBonds(mol)
# Fix structure to match the disulfide patching
if len(disulfide) != 0:
torem = np.zeros(mol.numAtoms, dtype=bool)
f.write("# Adding disulfide bonds\n")
for d in disulfide:
# Rename the residues to CYX if there is a disulfide bond
atoms1 = d[0].selectAtoms(mol, indexes=False)
atoms2 = d[1].selectAtoms(mol, indexes=False)
mol.resname[atoms1] = "CYX"
mol.resname[atoms2] = "CYX"
# Remove (eventual) HG hydrogens on these CYS (from proteinPrepare)
torem |= (atoms1 & (mol.name == "HG")) | (atoms2 &
(mol.name == "HG"))
# Convert to stupid amber residue numbering
uqseqid = (sequenceID(
(mol.resid, mol.insertion, mol.segid)) + mol.resid[0])
uqres1 = int(np.unique(uqseqid[atoms1]))
uqres2 = int(np.unique(uqseqid[atoms2]))
f.write(f"bond mol.{uqres1}.SG mol.{uqres2}.SG\n")
f.write("\n")
mol.remove(torem, _logger=False)
# Calculate the bounding box and store it in the CRD file
f.write('setBox mol "vdw"\n\n')
f.write("# Writing out the results\n")
f.write(f"saveamberparm mol {prefix}.prmtop {prefix}.crd\n")
f.write("quit")
f.close()
# Printing and loading the PDB file. AMBER can work with a single PDB file if the segments are separate by TER
logger.debug("Writing PDB file for input to tleap.")
pdbname = os.path.join(outdir, "input.pdb")
# mol2 files have atomtype, here we only write parts not coming from mol2
# We need to write the input.pdb at the end since we modify the resname for disulfide bridges in mol
mol.write(pdbname, mol.atomtype == "")
if not os.path.isfile(pdbname):
raise NameError(
"Could not write a PDB file out of the given Molecule.")
molbuilt = None
if execute:
if not teleapimports:
teleapimports = []
# Source default Amber (i.e. the same paths tleap imports)
amberhome = defaultAmberHome(teleap=teleap)
teleapimports += [
os.path.join(amberhome, s)
for s in _defaultAmberSearchPaths.values()
]
if len(teleapimports) == 0:
raise RuntimeWarning(
f"No default Amber force-field found. Check teLeap location: {teleap}"
)
# Source HTMD Amber paths that contain ffs
htmdamberdir = htmdAmberHome()
teleapimports += [
os.path.join(htmdamberdir, os.path.dirname(f)) for f in ff
if os.path.isfile(os.path.join(htmdamberdir, f))
]
if len(teleapimports) == 0:
raise RuntimeError(
"No default Amber force-field imports found. Check "
"`htmd.builder.amber.defaultAmberHome()` and `htmd.builder.amber.htmdAmberHome()`"
)
# Set import flags for teLeap
teleapimportflags = []
for p in teleapimports:
teleapimportflags.append("-I")
teleapimportflags.append(str(p))
logpath = os.path.abspath(os.path.join(outdir, "log.txt"))
logger.info("Starting the build.")
currdir = os.getcwd()
os.chdir(outdir)
f = open(logpath, "w")
try:
cmd = [teleap, "-f", "./tleap.in"]
cmd[1:1] = teleapimportflags
logger.debug(cmd)
call(cmd, stdout=f)
except:
raise NameError("teLeap failed at execution")
f.close()
errors = _logParser(logpath)
os.chdir(currdir)
if errors:
raise BuildError(errors + [
f"Check {logpath} for further information on errors in building."
])
logger.info("Finished building.")
if (os.path.exists(os.path.join(outdir, "structure.crd"))
and os.path.getsize(os.path.join(outdir, "structure.crd")) != 0
and os.path.getsize(os.path.join(outdir,
"structure.prmtop")) != 0):
try:
molbuilt = Molecule(os.path.join(outdir, "structure.prmtop"))
molbuilt.read(os.path.join(outdir, "structure.crd"))
except Exception as e:
raise RuntimeError(
f"Failed at reading structure.prmtop/structure.crd due to error: {e}"
)
else:
raise BuildError(
f"No structure pdb/prmtop file was generated. Check {logpath} for errors in building."
)
if ionize:
shutil.move(
os.path.join(outdir, "structure.crd"),
os.path.join(outdir, "structure.noions.crd"),
)
shutil.move(
os.path.join(outdir, "structure.prmtop"),
os.path.join(outdir, "structure.noions.prmtop"),
)
totalcharge = np.sum(molbuilt.charge)
nwater = np.sum(molbuilt.atomselect("water and noh"))
anion, cation, anionatom, cationatom, nanion, ncation = ionizef(
totalcharge,
nwater,
saltconc=saltconc,
anion=saltanion,
cation=saltcation,
)
newmol = ionizePlace(mol, anion, cation, anionatom, cationatom,
nanion, ncation)
# Redo the whole build but now with ions included
return build(
newmol,
ff=ff,
topo=topo,
param=param,
prefix=prefix,
outdir=outdir,
caps={},
ionize=False,
execute=execute,
saltconc=saltconc,
disulfide=disulfide,
teleap=teleap,
atomtypes=atomtypes,
offlibraries=offlibraries,
)
tmpbonds = molbuilt.bonds
molbuilt.bonds = [] # Removing the bonds to speed up writing
molbuilt.write(os.path.join(outdir, "structure.pdb"))
molbuilt.bonds = tmpbonds # Restoring the bonds
detectCisPeptideBonds(molbuilt) # Warn in case of cis bonds
return molbuilt
def build(
mol,
topo=None,
param=None,
stream=None,
prefix="structure",
outdir="./build",
caps=None,
ionize=True,
saltconc=0,
saltanion=None,
saltcation=None,
disulfide=None,
regenerate=["angles", "dihedrals"],
patches=None,
noregen=None,
aliasresidues=None,
psfgen=None,
execute=True,
_clean=True,
):
"""Builds a system for CHARMM
Uses VMD and psfgen to build a system for CHARMM. Additionally it allows for ionization and adding of disulfide bridges.
Parameters
----------
mol : :class:`Molecule <moleculekit.molecule.Molecule>` object
The Molecule object containing the system
topo : list of str
A list of topology `rtf` files.
Use :func:`charmm.listFiles <htmd.builder.charmm.listFiles>` to get a list of available topology files.
Default: ['top/top_all36_prot.rtf', 'top/top_all36_lipid.rtf', 'top/top_water_ions.rtf']
param : list of str
A list of parameter `prm` files.
Use :func:`charmm.listFiles <htmd.builder.charmm.listFiles>` to get a list of available parameter files.
Default: ['par/par_all36_prot.prm', 'par/par_all36_lipid.prm', 'par/par_water_ions.prm']
stream : list of str
A list of stream `str` files containing topologies and parameters.
Use :func:`charmm.listFiles <htmd.builder.charmm.listFiles>` to get a list of available stream files.
Default: ['str/prot/toppar_all36_prot_arg0.str']
prefix : str
The prefix for the generated pdb and psf files
outdir : str
The path to the output directory
Default: './build'
caps : dict
A dictionary with keys segids and values lists of strings describing the caps of that segment.
e.g. caps['P'] = ['first ACE', 'last CT3'] or caps['P'] = ['first none', 'last none'].
Default: will apply ACE and CT3 caps to proteins and none caps to the rest.
ionize : bool
Enable or disable ionization
saltconc : float
Salt concentration (in Molar) to add to the system after neutralization.
saltanion : {'CLA'}
The anion type. Please use only CHARMM ion atom names.
saltcation : {'SOD', 'MG', 'POT', 'CES', 'CAL', 'ZN2'}
The cation type. Please use only CHARMM ion atom names.
disulfide : list of pairs of atomselection strings
If None it will guess disulfide bonds. Otherwise provide a list pairs of atomselection strings for each pair of
residues forming the disulfide bridge.
regenerate : None or list of strings of: ['angles', 'dihedrals']
Disable angle/dihedral regeneration with `regenerate=None`, or enable it with `regenerate=['angles', 'diheldrals']`
or just one of the two options with `regenerate=['angles']` or `regenerate=['diheldrals']`.
patches : list of str
Any further patches the user wants to apply
noregen : list of str
A list of patches that must not be regenerated (angles and dihedrals)
Default: ['FHEM', 'PHEM', 'PLOH', 'PLO2', 'PLIG', 'PSUL']
aliasresidues : dict of aliases
A dictionary of key: value pairs of residue names we want to alias
psfgen : str
Path to psfgen executable used to build for CHARMM
execute : bool
Disable building. Will only write out the input script needed by psfgen. Does not include ionization.
Returns
-------
molbuilt : :class:`Molecule <moleculekit.molecule.Molecule>` object
The built system in a Molecule object
Example
-------
>>> from htmd.ui import *
>>> mol = Molecule("3PTB")
>>> mol.filter("not resname BEN")
>>> molbuilt = charmm.build(mol, outdir='/tmp/build', ionize=False) # doctest: +ELLIPSIS
Bond between A: [serial 185 resid 42 resname CYS chain A segid 0]
B: [serial 298 resid 58 resname CYS chain A segid 0]...
>>> # More complex example
>>> topos = ['top/top_all36_prot.rtf', './BEN.rtf', 'top/top_water_ions.rtf']
>>> params = ['par/par_all36_prot.prm', './BEN.prm', 'par/par_water_ions.prm']
>>> disu = [['segid P and resid 157', 'segid P and resid 13'], ['segid K and resid 1', 'segid K and resid 25']]
>>> ar = {'SAPI24': 'SP24'} # Alias large resnames to a short-hand version
>>> molbuilt = charmm.build(mol, topo=topos, param=params, outdir='/tmp/build', saltconc=0.15, disulfide=disu, aliasresidues=ar) # doctest: +SKIP
"""
mol = mol.copy()
_missingSegID(mol)
_checkMixedSegment(mol)
_checkLongResnames(mol, aliasresidues)
if psfgen is None:
psfgen = shutil.which("psfgen", mode=os.X_OK)
if not psfgen:
raise FileNotFoundError(
"Could not find psfgen executable, or no execute permissions are given. "
"Run `conda install psfgen -c acellera`.")
if not os.path.isdir(outdir):
os.makedirs(outdir)
if _clean:
_cleanOutDir(outdir)
if topo is None:
topo = defaultTopo()
if param is None:
param = defaultParam()
if stream is None:
stream = defaultStream()
if caps is None:
caps = _defaultCaps(mol)
# patches that must _not_ be regenerated
if noregen is None:
noregen = ["FHEM", "PHEM", "PLOH", "PLO2", "PLIG", "PSUL"]
alltopo = topo.copy()
allparam = param.copy()
# Splitting the stream files and adding them to the list of parameter and topology files
charmmdir = htmdCharmmHome()
for s in stream:
if s[0] != "." and path.isfile(path.join(charmmdir, s)):
s = path.join(charmmdir, s)
outrtf, outprm = _prepareStream(s)
alltopo.append(outrtf)
allparam.append(outprm)
# _missingChain(mol)
# _checkProteinGaps(mol)
if patches is None:
patches = []
if isinstance(patches, str):
patches = [patches]
allpatches = []
allpatches += patches
# Find protonated residues and add patches for them
allpatches += _protonationPatches(mol)
f = open(path.join(outdir, "build.vmd"), "w")
f.write("# psfgen file generated by charmm.build\n")
f.write("package require psfgen;\n")
f.write("psfcontext reset;\n\n")
# Copying and printing out the topologies
if not path.exists(path.join(outdir, "topologies")):
os.makedirs(path.join(outdir, "topologies"))
for i in range(len(alltopo)):
if alltopo[i][0] != "." and path.isfile(
path.join(charmmdir, alltopo[i])):
alltopo[i] = path.join(charmmdir, alltopo[i])
localname = "{}.".format(i) + path.basename(alltopo[i])
shutil.copy(alltopo[i], path.join(outdir, "topologies", localname))
f.write("topology " + path.join("topologies", localname) + "\n")
f.write("\n")
_printAliases(f)
if aliasresidues is not None: # User defined aliases
for key, val in aliasresidues.items():
mol.resname[mol.resname == key] = val
f.write(" pdbalias residue {} {}\n".format(val, key))
# Printing out segments
if not path.exists(path.join(outdir, "segments")):
os.makedirs(path.join(outdir, "segments"))
logger.info("Writing out segments.")
segments = _getSegments(mol)
wateratoms = mol.atomselect("water")
for seg in segments:
pdbname = "segment" + seg + ".pdb"
segatoms = mol.segid == seg
mol.write(path.join(outdir, "segments", pdbname), sel=segatoms)
segwater = wateratoms & segatoms
f.write("segment " + seg + " {\n")
if np.all(segatoms ==
segwater): # If segment only contains waters, set: auto none
f.write("\tauto none\n")
f.write("\tpdb " + path.join("segments", pdbname) + "\n")
if caps is not None and seg in caps:
for c in caps[seg]:
f.write("\t" + c + "\n")
f.write("}\n")
f.write("coordpdb " + path.join("segments", pdbname) + " " + seg +
"\n\n")
if (disulfide is not None and len(disulfide) != 0
and isinstance(disulfide[0][0], str)):
disulfide = convertDisulfide(mol, disulfide)
if disulfide is None:
disulfide = detectDisulfideBonds(mol)
if len(disulfide) != 0:
for d in sorted(disulfide, key=lambda x: x[0].segid):
str0 = f"{d[0].segid}:{d[0].resid}{d[0].insertion}"
str1 = f"{d[1].segid}:{d[1].resid}{d[1].insertion}"
f.write(f"patch DISU {str0} {str1}\n")
f.write("\n")
noregenpatches = [p for p in allpatches if p.split()[1] in noregen]
regenpatches = [p for p in allpatches if p.split()[1] not in noregen]
# Printing regenerable patches
if len(regenpatches) != 0:
for p in regenpatches:
f.write(p + "\n")
f.write("\n")
# Regenerate angles and dihedrals
if regenerate is not None:
f.write("regenerate {}\n".format(" ".join(regenerate)))
f.write("\n")
# Printing non-regenerable patches
if len(noregenpatches) != 0:
for p in noregenpatches:
f.write(p + "\n")
f.write("\n")
f.write("guesscoord\n")
f.write("writepsf " + prefix + ".psf\n")
f.write("writepdb " + prefix + ".pdb\n")
# f.write('quit\n')
f.close()
if allparam is not None:
combine(allparam, path.join(outdir, "parameters"))
molbuilt = None
if execute:
logpath = os.path.abspath("{}/log.txt".format(outdir))
logger.info("Starting the build.")
currdir = os.getcwd()
os.chdir(outdir)
f = open(logpath, "w")
# call([vmd, '-dispdev', 'text', '-e', './build.vmd'], stdout=f)
my_env = os.environ.copy()
my_env["LC_ALL"] = "C"
call([psfgen, "./build.vmd"], stdout=f, stderr=f, env=my_env)
f.close()
errors = _logParser(logpath)
os.chdir(currdir)
if errors:
raise BuildError(errors + [
"Check {} for further information on errors in building.".
format(logpath)
])
logger.info("Finished building.")
if path.isfile(path.join(outdir, "structure.pdb")) and path.isfile(
path.join(outdir, "structure.psf")):
molbuilt = Molecule(path.join(outdir, "structure.pdb"))
molbuilt.read(path.join(outdir, "structure.psf"))
else:
raise BuildError(
"No structure pdb/psf file was generated. Check {} for errors in building."
.format(logpath))
if ionize:
os.makedirs(path.join(outdir, "pre-ionize"))
data = glob(path.join(outdir, "*"))
for f in data:
shutil.move(f, path.join(outdir, "pre-ionize"))
totalcharge = np.sum(molbuilt.charge)
nwater = np.sum(molbuilt.atomselect("water and noh"))
anion, cation, anionatom, cationatom, nanion, ncation = ionizef(
molbuilt,
totalcharge,
nwater,
saltconc=saltconc,
anion=saltanion,
cation=saltcation,
)
newmol = ionizePlace(mol, anion, cation, anionatom, cationatom,
nanion, ncation)
# Redo the whole build but now with ions included
return build(
newmol,
topo=alltopo,
param=allparam,
stream=[],
prefix=prefix,
outdir=outdir,
ionize=False,
caps=caps,
execute=execute,
saltconc=saltconc,
disulfide=disulfide,
regenerate=regenerate,
patches=patches,
noregen=noregen,
aliasresidues=aliasresidues,
psfgen=psfgen,
_clean=False,
)
_checkFailedAtoms(molbuilt)
_recoverProtonations(molbuilt)
detectCisPeptideBonds(molbuilt,
respect_bonds=True) # Warn in case of cis bonds
return molbuilt