def test2(a,radius,box=100.0,fbase=None):
# l.test2(5.0797,15)
if fbase is None:
fbase = "{}_{}".format(box,radius)
top = "{}.top".format(fbase)
struct = "{}.pdb".format(fbase)
sol = "{}.sol.pdb".format(fbase)
ndx = "{}.ndx".format(fbase)
origin = box/2.
pts=fcc_sphere(a, radius)
w=writer("{}.pdb".format(fbase))
w.CRYST1([box,box,box,90.00,90.00,90.00])
for index,atom in enumerate(pts):
w.ATOM(serial=index+1, name="AU", resName="NP", resSeq=1,
chainID="A", segID="AUNP", element="AU",
x=atom[0]+origin, y=atom[1]+origin, z=atom[2]+origin)
w.close()
#make_index("{}.pdb".format(fbase), "{}.ndx".format(fbase))
with file(top, "w") as t:
t.write(top_src)
t.write("Au {}\n".format(pts.shape[0]))
gromacs.genbox(p=top, cp=struct, cs="spc216.gro", o=sol, vdwd="0.15") #@UndefinedVariable
rc,out,nothing = gromacs.make_ndx(f=sol, n=None, o=ndx, stdout=False, #@UndefinedVariable
input=('', '', 'q'))
gromacs.grompp(f="md2.mdp", o="{}.tpr".format(fbase), c=sol, p=top, n=ndx) #@UndefinedVariable
with file("{}.sh".format(fbase), "w") as f:
f.write("#!/bin/bash\n")
f.write("#PBS -k o\n")
f.write("#PBS -l nodes=1:ppn=12:ccvt,walltime=24:00:00\n")
f.write("#PBS -M [email protected]\n")
f.write("#PBS -m abe\n")
f.write("#PBS -N {}\n".format(fbase))
f.write("#PBS -j oe\n")
f.write("#PBS -q pg\n")
f.write("#PBS -d /N/dc/scratch/somogyie/Au\n")
f.write("mpirun mdrun -deffnm {}".format(fbase))
def solvate(struct='top/protein.pdb',
top='top/system.top',
distance=0.9,
boxtype='dodecahedron',
concentration=0,
cation='NA',
anion='CL',
water='spc',
solvent_name='SOL',
with_membrane=False,
ndx='main.ndx',
mainselection='"Protein"',
dirname='solvate',
**kwargs):
"""Put protein into box, add water, add counter-ions.
Currently this really only supports solutes in water. If you need
to embedd a protein in a membrane then you will require more
sophisticated approaches.
However, you *can* supply a protein already inserted in a
bilayer. In this case you will probably want to set *distance* =
``None`` and also enable *with_membrane* = ``True`` (using extra
big vdw radii for typical lipids).
.. Note:: The defaults are suitable for solvating a globular
protein in a fairly tight (increase *distance*!) dodecahedral
box.
:Arguments:
*struct* : filename
pdb or gro input structure
*top* : filename
Gromacs topology
*distance* : float
When solvating with water, make the box big enough so that
at least *distance* nm water are between the solute *struct*
and the box boundary.
Set *boxtype* to ``None`` in order to use a box size in the input
file (gro or pdb).
*boxtype* or *bt*: string
Any of the box types supported by :class:`~gromacs.tools.Editconf`
(triclinic, cubic, dodecahedron, octahedron). Set the box dimensions
either with *distance* or the *box* and *angle* keywords.
If set to ``None`` it will ignore *distance* and use the box
inside the *struct* file.
*bt* overrides the value of *boxtype*.
*box*
List of three box lengths [A,B,C] that are used by :class:`~gromacs.tools.Editconf`
in combination with *boxtype* (``bt`` in :program:`editconf`) and *angles*.
Setting *box* overrides *distance*.
*angles*
List of three angles (only necessary for triclinic boxes).
*concentration* : float
Concentration of the free ions in mol/l. Note that counter
ions are added in excess of this concentration.
*cation* and *anion* : string
Molecule names of the ions. This depends on the chosen force field.
*water* : string
Name of the water model; one of "spc", "spce", "tip3p",
"tip4p". This should be appropriate for the chosen force
field. If an alternative solvent is required, simply supply the path to a box
with solvent molecules (used by :func:`~gromacs.genbox`'s *cs* argument)
and also supply the molecule name via *solvent_name*.
*solvent_name*
Name of the molecules that make up the solvent (as set in the itp/top).
Typically needs to be changed when using non-standard/non-water solvents.
["SOL"]
*with_membrane* : bool
``True``: use special ``vdwradii.dat`` with 0.1 nm-increased radii on
lipids. Default is ``False``.
*ndx* : filename
How to name the index file that is produced by this function.
*mainselection* : string
A string that is fed to :class:`~gromacs.tools.Make_ndx` and
which should select the solute.
*dirname* : directory name
Name of the directory in which all files for the solvation stage are stored.
*includes*
List of additional directories to add to the mdp include path
*kwargs*
Additional arguments are passed on to
:class:`~gromacs.tools.Editconf` or are interpreted as parameters to be
changed in the mdp file.
"""
structure = realpath(struct)
topology = realpath(top)
# arguments for editconf that we honour
editconf_keywords = [
"box", "bt", "angles", "c", "center", "aligncenter", "align",
"translate", "rotate", "princ"
]
editconf_kwargs = dict((k, kwargs.pop(k, None)) for k in editconf_keywords)
editconf_boxtypes = [
"triclinic", "cubic", "dodecahedron", "octahedron", None
]
# needed for topology scrubbing
scrubber_kwargs = {'marker': kwargs.pop('marker', None)}
# sanity checks and argument dependencies
bt = editconf_kwargs.pop('bt')
boxtype = bt if bt else boxtype # bt takes precedence over boxtype
if not boxtype in editconf_boxtypes:
msg = "Unsupported boxtype {boxtype!r}: Only {boxtypes!r} are possible.".format(
**vars())
logger.error(msg)
raise ValueError(msg)
if editconf_kwargs['box']:
distance = None # if box is set then user knows what she is doing...
# handle additional include directories (kwargs are also modified!)
mdp_kwargs = cbook.add_mdp_includes(topology, kwargs)
if water.lower() in ('spc', 'spce'):
water = 'spc216'
elif water.lower() == 'tip3p':
water = 'spc216'
logger.warning(
"TIP3P water model selected: using SPC equilibrated box "
"for initial solvation because it is a reasonable starting point "
"for any 3-point model. EQUILIBRATE THOROUGHLY!")
# By default, grompp should not choke on a few warnings because at
# this stage the user cannot do much about it (can be set to any
# value but is kept undocumented...)
grompp_maxwarn = kwargs.pop('maxwarn', 10)
# clean topology (if user added the marker; the default marker is
# ; Gromacs auto-generated entries follow:
n_removed = cbook.remove_molecules_from_topology(topology,
**scrubber_kwargs)
with in_dir(dirname):
logger.info(
"[{dirname!s}] Solvating with water {water!r}...".format(**vars()))
if boxtype is None:
hasBox = False
ext = os.path.splitext(structure)[1]
if ext == '.gro':
hasBox = True
elif ext == '.pdb':
with open(structure) as struct:
for line in struct:
if line.startswith('CRYST'):
hasBox = True
break
if not hasBox:
msg = "No box data in the input structure {structure!r} and boxtype is set to None".format(
**vars())
logger.exception(msg)
raise MissingDataError(msg)
distance = boxtype = None # ensures that editconf just converts
editconf_kwargs.update({
'f': structure,
'o': 'boxed.gro',
'bt': boxtype,
'd': distance
})
gromacs.editconf(**editconf_kwargs)
if with_membrane:
vdwradii_dat = get_lipid_vdwradii() # need to clean up afterwards
logger.info("Using special vdW radii for lipids {0!r}".format(
vdw_lipid_resnames))
try:
gromacs.genbox(p=topology,
cp='boxed.gro',
cs=water,
o='solvated.gro')
except:
if with_membrane:
# remove so that it's not picked up accidentally
utilities.unlink_f(vdwradii_dat)
raise
logger.info("Solvated system with %s", water)
with open('none.mdp', 'w') as mdp:
mdp.write(
'; empty mdp file\ninclude = {include!s}\nrcoulomb = 1\nrvdw = 1\nrlist = 1\n'
.format(**mdp_kwargs))
qtotgmx = cbook.grompp_qtot(f='none.mdp',
o='topol.tpr',
c='solvated.gro',
p=topology,
stdout=False,
maxwarn=grompp_maxwarn)
qtot = round(qtotgmx)
logger.info(
"[{dirname!s}] After solvation: total charge qtot = {qtotgmx!r} = {qtot!r}"
.format(**vars()))
if concentration != 0:
logger.info(
"[{dirname!s}] Adding ions for c = {concentration:f} M...".
format(**vars()))
# target concentration of free ions c ==>
# N = N_water * c/c_water
# add ions for concentration to the counter ions (counter ions are less free)
#
# get number of waters (count OW ... works for SPC*, TIP*P water models)
rc, output, junk = gromacs.make_ndx(f='topol.tpr',
o='ow.ndx',
input=('keep 0', 'del 0',
'a OW*', 'name 0 OW',
'', 'q'),
stdout=False)
groups = cbook.parse_ndxlist(output)
gdict = {g['name']: g for g in groups} # overkill...
N_water = gdict['OW']['natoms'] # ... but dict lookup is nice
N_ions = int(N_water * concentration /
CONC_WATER) # number of monovalents
else:
N_ions = 0
# neutralize (or try -neutral switch of genion???)
n_cation = n_anion = 0
if qtot > 0:
n_anion = int(abs(qtot))
elif qtot < 0:
n_cation = int(abs(qtot))
n_cation += N_ions
n_anion += N_ions
if n_cation != 0 or n_anion != 0:
# sanity check:
assert qtot + n_cation - n_anion < 1e-6
logger.info(
"[{dirname!s}] Adding n_cation = {n_cation:d} and n_anion = {n_anion:d} ions..."
.format(**vars()))
gromacs.genion(s='topol.tpr',
o='ionized.gro',
p=topology,
pname=cation,
nname=anion,
np=n_cation,
nn=n_anion,
input=solvent_name)
else:
# fake ionized file ... makes it easier to continue without too much fuzz
try:
os.unlink('ionized.gro')
except OSError, err:
if err.errno != errno.ENOENT:
raise
os.symlink('solvated.gro', 'ionized.gro')
qtot = cbook.grompp_qtot(f='none.mdp',
o='ionized.tpr',
c='ionized.gro',
p=topology,
stdout=False,
maxwarn=grompp_maxwarn)
if abs(qtot) > 1e-4:
wmsg = "System has non-zero total charge qtot = {qtot:g} e.".format(
**vars())
warnings.warn(wmsg, category=BadParameterWarning)
logger.warn(wmsg)
# make main index
try:
make_main_index('ionized.tpr', selection=mainselection, ndx=ndx)
except GromacsError, err:
# or should I rather fail here?
wmsg = "Failed to make main index file %r ... maybe set mainselection='...'.\n"\
"The error message was:\n%s\n" % (ndx, str(err))
logger.warn(wmsg)
warnings.warn(wmsg, category=GromacsFailureWarning)
def solvate(struct='top/protein.pdb', top='top/system.top',
distance=0.9, boxtype='dodecahedron',
concentration=0, cation='NA', anion='CL',
water='spc', solvent_name='SOL', with_membrane=False,
ndx = 'main.ndx', mainselection = '"Protein"',
dirname='solvate',
**kwargs):
"""Put protein into box, add water, add counter-ions.
Currently this really only supports solutes in water. If you need
to embedd a protein in a membrane then you will require more
sophisticated approaches.
However, you *can* supply a protein already inserted in a
bilayer. In this case you will probably want to set *distance* =
``None`` and also enable *with_membrane* = ``True`` (using extra
big vdw radii for typical lipids).
.. Note:: The defaults are suitable for solvating a globular
protein in a fairly tight (increase *distance*!) dodecahedral
box.
:Arguments:
*struct* : filename
pdb or gro input structure
*top* : filename
Gromacs topology
*distance* : float
When solvating with water, make the box big enough so that
at least *distance* nm water are between the solute *struct*
and the box boundary.
Set *boxtype* to ``None`` in order to use a box size in the input
file (gro or pdb).
*boxtype* or *bt*: string
Any of the box types supported by :class:`~gromacs.tools.Editconf`
(triclinic, cubic, dodecahedron, octahedron). Set the box dimensions
either with *distance* or the *box* and *angle* keywords.
If set to ``None`` it will ignore *distance* and use the box
inside the *struct* file.
*bt* overrides the value of *boxtype*.
*box*
List of three box lengths [A,B,C] that are used by :class:`~gromacs.tools.Editconf`
in combination with *boxtype* (``bt`` in :program:`editconf`) and *angles*.
Setting *box* overrides *distance*.
*angles*
List of three angles (only necessary for triclinic boxes).
*concentration* : float
Concentration of the free ions in mol/l. Note that counter
ions are added in excess of this concentration.
*cation* and *anion* : string
Molecule names of the ions. This depends on the chosen force field.
*water* : string
Name of the water model; one of "spc", "spce", "tip3p",
"tip4p". This should be appropriate for the chosen force
field. If an alternative solvent is required, simply supply the path to a box
with solvent molecules (used by :func:`~gromacs.genbox`'s *cs* argument)
and also supply the molecule name via *solvent_name*.
*solvent_name*
Name of the molecules that make up the solvent (as set in the itp/top).
Typically needs to be changed when using non-standard/non-water solvents.
["SOL"]
*with_membrane* : bool
``True``: use special ``vdwradii.dat`` with 0.1 nm-increased radii on
lipids. Default is ``False``.
*ndx* : filename
How to name the index file that is produced by this function.
*mainselection* : string
A string that is fed to :class:`~gromacs.tools.Make_ndx` and
which should select the solute.
*dirname* : directory name
Name of the directory in which all files for the solvation stage are stored.
*includes*
List of additional directories to add to the mdp include path
*kwargs*
Additional arguments are passed on to
:class:`~gromacs.tools.Editconf` or are interpreted as parameters to be
changed in the mdp file.
"""
structure = realpath(struct)
topology = realpath(top)
# arguments for editconf that we honour
editconf_keywords = ["box", "bt", "angles", "c", "center", "aligncenter",
"align", "translate", "rotate", "princ"]
editconf_kwargs = dict((k,kwargs.pop(k,None)) for k in editconf_keywords)
editconf_boxtypes = ["triclinic", "cubic", "dodecahedron", "octahedron", None]
# needed for topology scrubbing
scrubber_kwargs = {'marker': kwargs.pop('marker',None)}
# sanity checks and argument dependencies
bt = editconf_kwargs.pop('bt')
boxtype = bt if bt else boxtype # bt takes precedence over boxtype
if not boxtype in editconf_boxtypes:
msg = "Unsupported boxtype {boxtype!r}: Only {boxtypes!r} are possible.".format(**vars())
logger.error(msg)
raise ValueError(msg)
if editconf_kwargs['box']:
distance = None # if box is set then user knows what she is doing...
# handle additional include directories (kwargs are also modified!)
mdp_kwargs = cbook.add_mdp_includes(topology, kwargs)
if water.lower() in ('spc', 'spce'):
water = 'spc216'
elif water.lower() == 'tip3p':
water = 'spc216'
logger.warning("TIP3P water model selected: using SPC equilibrated box "
"for initial solvation because it is a reasonable starting point "
"for any 3-point model. EQUILIBRATE THOROUGHLY!")
# By default, grompp should not choke on a few warnings because at
# this stage the user cannot do much about it (can be set to any
# value but is kept undocumented...)
grompp_maxwarn = kwargs.pop('maxwarn',10)
# clean topology (if user added the marker; the default marker is
# ; Gromacs auto-generated entries follow:
n_removed = cbook.remove_molecules_from_topology(topology, **scrubber_kwargs)
with in_dir(dirname):
logger.info("[{dirname!s}] Solvating with water {water!r}...".format(**vars()))
if boxtype is None:
hasBox = False
ext = os.path.splitext(structure)[1]
if ext == '.gro':
hasBox = True
elif ext == '.pdb':
with open(structure) as struct:
for line in struct:
if line.startswith('CRYST'):
hasBox = True
break
if not hasBox:
msg = "No box data in the input structure {structure!r} and boxtype is set to None".format(**vars())
logger.exception(msg)
raise MissingDataError(msg)
distance = boxtype = None # ensures that editconf just converts
editconf_kwargs.update({'f': structure, 'o': 'boxed.gro',
'bt': boxtype, 'd': distance})
gromacs.editconf(**editconf_kwargs)
if with_membrane:
vdwradii_dat = get_lipid_vdwradii() # need to clean up afterwards
logger.info("Using special vdW radii for lipids {0!r}".format(vdw_lipid_resnames))
try:
gromacs.genbox(p=topology, cp='boxed.gro', cs=water, o='solvated.gro')
except:
if with_membrane:
# remove so that it's not picked up accidentally
utilities.unlink_f(vdwradii_dat)
raise
logger.info("Solvated system with %s", water)
with open('none.mdp','w') as mdp:
mdp.write('; empty mdp file\ninclude = {include!s}\nrcoulomb = 1\nrvdw = 1\nrlist = 1\n'.format(**mdp_kwargs))
qtotgmx = cbook.grompp_qtot(f='none.mdp', o='topol.tpr', c='solvated.gro',
p=topology, stdout=False, maxwarn=grompp_maxwarn)
qtot = round(qtotgmx)
logger.info("[{dirname!s}] After solvation: total charge qtot = {qtotgmx!r} = {qtot!r}".format(**vars()))
if concentration != 0:
logger.info("[{dirname!s}] Adding ions for c = {concentration:f} M...".format(**vars()))
# target concentration of free ions c ==>
# N = N_water * c/c_water
# add ions for concentration to the counter ions (counter ions are less free)
#
# get number of waters (count OW ... works for SPC*, TIP*P water models)
rc,output,junk = gromacs.make_ndx(f='topol.tpr', o='ow.ndx',
input=('keep 0', 'del 0', 'a OW*', 'name 0 OW', '', 'q'),
stdout=False)
groups = cbook.parse_ndxlist(output)
gdict = {g['name']: g for g in groups} # overkill...
N_water = gdict['OW']['natoms'] # ... but dict lookup is nice
N_ions = int(N_water * concentration/CONC_WATER) # number of monovalents
else:
N_ions = 0
# neutralize (or try -neutral switch of genion???)
n_cation = n_anion = 0
if qtot > 0:
n_anion = int(abs(qtot))
elif qtot < 0:
n_cation = int(abs(qtot))
n_cation += N_ions
n_anion += N_ions
if n_cation != 0 or n_anion != 0:
# sanity check:
assert qtot + n_cation - n_anion < 1e-6
logger.info("[{dirname!s}] Adding n_cation = {n_cation:d} and n_anion = {n_anion:d} ions...".format(**vars()))
gromacs.genion(s='topol.tpr', o='ionized.gro', p=topology,
pname=cation, nname=anion, np=n_cation, nn=n_anion,
input=solvent_name)
else:
# fake ionized file ... makes it easier to continue without too much fuzz
try:
os.unlink('ionized.gro')
except OSError, err:
if err.errno != errno.ENOENT:
raise
os.symlink('solvated.gro', 'ionized.gro')
qtot = cbook.grompp_qtot(f='none.mdp', o='ionized.tpr', c='ionized.gro',
p=topology, stdout=False, maxwarn=grompp_maxwarn)
if abs(qtot) > 1e-4:
wmsg = "System has non-zero total charge qtot = {qtot:g} e.".format(**vars())
warnings.warn(wmsg, category=BadParameterWarning)
logger.warn(wmsg)
# make main index
try:
make_main_index('ionized.tpr', selection=mainselection, ndx=ndx)
except GromacsError, err:
# or should I rather fail here?
wmsg = "Failed to make main index file %r ... maybe set mainselection='...'.\n"\
"The error message was:\n%s\n" % (ndx, str(err))
logger.warn(wmsg)
warnings.warn(wmsg, category=GromacsFailureWarning)
def test2(a, radius, box=100.0, fbase=None):
# l.test2(5.0797,15)
if fbase is None:
fbase = "{}_{}".format(box, radius)
top = "{}.top".format(fbase)
struct = "{}.pdb".format(fbase)
sol = "{}.sol.pdb".format(fbase)
ndx = "{}.ndx".format(fbase)
origin = box / 2.
pts = fcc_sphere(a, radius)
w = writer("{}.pdb".format(fbase))
w.CRYST1([box, box, box, 90.00, 90.00, 90.00])
for index, atom in enumerate(pts):
w.ATOM(serial=index + 1,
name="AU",
resName="NP",
resSeq=1,
chainID="A",
segID="AUNP",
element="AU",
x=atom[0] + origin,
y=atom[1] + origin,
z=atom[2] + origin)
w.close()
#make_index("{}.pdb".format(fbase), "{}.ndx".format(fbase))
with file(top, "w") as t:
t.write(top_src)
t.write("Au {}\n".format(pts.shape[0]))
gromacs.genbox(p=top, cp=struct, cs="spc216.gro", o=sol,
vdwd="0.15") #@UndefinedVariable
rc, out, nothing = gromacs.make_ndx(
f=sol,
n=None,
o=ndx,
stdout=False, #@UndefinedVariable
input=('', '', 'q'))
gromacs.grompp(f="md2.mdp", o="{}.tpr".format(fbase), c=sol, p=top,
n=ndx) #@UndefinedVariable
with file("{}.sh".format(fbase), "w") as f:
f.write("#!/bin/bash\n")
f.write("#PBS -k o\n")
f.write("#PBS -l nodes=1:ppn=12:ccvt,walltime=24:00:00\n")
f.write("#PBS -M [email protected]\n")
f.write("#PBS -m abe\n")
f.write("#PBS -N {}\n".format(fbase))
f.write("#PBS -j oe\n")
f.write("#PBS -q pg\n")
f.write("#PBS -d /N/dc/scratch/somogyie/Au\n")
f.write("mpirun mdrun -deffnm {}".format(fbase))
def solvate_sol(struct='top/protein.pdb',
top='top/system.top',
distance=0.9,
boxtype='dodecahedron',
water='tip4p',
solvent_name='SOL',
with_membrane=False,
dirname='solvate',
**kwargs):
structure = realpath(struct)
topology = realpath(top)
# arguments for editconf that we honour
editconf_keywords = [
"box", "bt", "angles", "c", "center", "aligncenter", "align",
"translate", "rotate", "princ"
]
editconf_kwargs = dict((k, kwargs.pop(k, None)) for k in editconf_keywords)
editconf_boxtypes = [
"triclinic", "cubic", "dodecahedron", "octahedron", None
]
# needed for topology scrubbing
scrubber_kwargs = {'marker': kwargs.pop('marker', None)}
# sanity checks and argument dependencies
bt = editconf_kwargs.pop('bt')
boxtype = bt if bt else boxtype # bt takes precedence over boxtype
if not boxtype in editconf_boxtypes:
msg = "Unsupported boxtype {boxtype!r}: Only {boxtypes!r} are possible.".format(
**vars())
logger.error(msg)
raise ValueError(msg)
if editconf_kwargs['box']:
distance = None # if box is set then user knows what she is doing...
if water.lower() in ('spc', 'spce'):
water = 'spc216'
elif water.lower() == 'tip3p':
water = 'spc216'
logger.warning(
"TIP3P water model selected: using SPC equilibrated box "
"for initial solvation because it is a reasonable starting point "
"for any 3-point model. EQUILIBRATE THOROUGHLY!")
# clean topology (if user added the marker; the default marker is
# ; Gromacs auto-generated entries follow:
n_removed = cbook.remove_molecules_from_topology(topology,
**scrubber_kwargs)
with in_dir(dirname):
logger.info(
"[{dirname!s}] Solvating with water {water!r}...".format(**vars()))
if boxtype is None:
hasBox = False
ext = os.path.splitext(structure)[1]
if ext == '.gro':
hasBox = True
elif ext == '.pdb':
with open(structure) as struct:
for line in struct:
if line.startswith('CRYST'):
hasBox = True
break
if not hasBox:
msg = "No box data in the input structure {structure!r} and boxtype is set to None".format(
**vars())
logger.exception(msg)
raise MissingDataError(msg)
distance = boxtype = None # ensures that editconf just converts
editconf_kwargs.update({
'f': structure,
'o': 'boxed.gro',
'bt': boxtype,
'd': distance
})
gromacs.editconf(**editconf_kwargs)
if with_membrane:
vdwradii_dat = get_lipid_vdwradii() # need to clean up afterwards
logger.info("Using special vdW radii for lipids {0!r}".format(
vdw_lipid_resnames))
try:
gromacs.genbox(p=topology,
cp='boxed.gro',
cs=water,
o='solvated.gro')
except:
if with_membrane:
# remove so that it's not picked up accidentally
utilities.unlink_f(vdwradii_dat)
raise
logger.info("Solvated system with %s", water)
return {
'struct': realpath(dirname, 'solvated.gro'),
}
def solvate_sol(struct='top/protein.pdb', top='top/system.top',
distance=0.9, boxtype='dodecahedron',
water='tip4p', solvent_name='SOL', with_membrane=False,
dirname='solvate',
**kwargs):
structure = realpath(struct)
topology = realpath(top)
# arguments for editconf that we honour
editconf_keywords = ["box", "bt", "angles", "c", "center", "aligncenter",
"align", "translate", "rotate", "princ"]
editconf_kwargs = dict((k,kwargs.pop(k,None)) for k in editconf_keywords)
editconf_boxtypes = ["triclinic", "cubic", "dodecahedron", "octahedron", None]
# needed for topology scrubbing
scrubber_kwargs = {'marker': kwargs.pop('marker',None)}
# sanity checks and argument dependencies
bt = editconf_kwargs.pop('bt')
boxtype = bt if bt else boxtype # bt takes precedence over boxtype
if not boxtype in editconf_boxtypes:
msg = "Unsupported boxtype {boxtype!r}: Only {boxtypes!r} are possible.".format(**vars())
logger.error(msg)
raise ValueError(msg)
if editconf_kwargs['box']:
distance = None # if box is set then user knows what she is doing...
if water.lower() in ('spc', 'spce'):
water = 'spc216'
elif water.lower() == 'tip3p':
water = 'spc216'
logger.warning("TIP3P water model selected: using SPC equilibrated box "
"for initial solvation because it is a reasonable starting point "
"for any 3-point model. EQUILIBRATE THOROUGHLY!")
# clean topology (if user added the marker; the default marker is
# ; Gromacs auto-generated entries follow:
n_removed = cbook.remove_molecules_from_topology(topology, **scrubber_kwargs)
with in_dir(dirname):
logger.info("[{dirname!s}] Solvating with water {water!r}...".format(**vars()))
if boxtype is None:
hasBox = False
ext = os.path.splitext(structure)[1]
if ext == '.gro':
hasBox = True
elif ext == '.pdb':
with open(structure) as struct:
for line in struct:
if line.startswith('CRYST'):
hasBox = True
break
if not hasBox:
msg = "No box data in the input structure {structure!r} and boxtype is set to None".format(**vars())
logger.exception(msg)
raise MissingDataError(msg)
distance = boxtype = None # ensures that editconf just converts
editconf_kwargs.update({'f': structure, 'o': 'boxed.gro',
'bt': boxtype, 'd': distance})
gromacs.editconf(**editconf_kwargs)
if with_membrane:
vdwradii_dat = get_lipid_vdwradii() # need to clean up afterwards
logger.info("Using special vdW radii for lipids {0!r}".format(vdw_lipid_resnames))
try:
gromacs.genbox(p=topology, cp='boxed.gro', cs=water, o='solvated.gro')
except:
if with_membrane:
# remove so that it's not picked up accidentally
utilities.unlink_f(vdwradii_dat)
raise
logger.info("Solvated system with %s", water)
return {'struct': realpath(dirname, 'solvated.gro'),}
