def main(opt):
# Check all of the arguments
if not os.path.exists(opt.prmtop):
raise AmberError('prmtop file (%s) is missing' % opt.prmtop)
# Process the arguments that take multiple args
resstates = process_arglist(opt.resstates, int)
resnums = process_arglist(opt.resnums, int)
notresnums = process_arglist(opt.notresnums, int)
resnames = process_arglist(opt.resnames, str)
notresnames = process_arglist(opt.notresnames, str)
minpka = opt.minpka
maxpka = opt.maxpka
if not opt.igb in (1, 2, 5, 7, 8):
raise AmberError('-igb must be 1, 2, 5, 7, or 8!')
if resnums is not None and notresnums is not None:
raise AmberError('Cannot specify -resnums and -notresnums together')
if resnames is not None and notresnames is not None:
raise AmberError('Cannot specify -resnames and -notresnames together')
if opt.intdiel != 1 and opt.intdiel != 2:
raise AmberError('-intdiel must be either 1 or 2 currently')
# Print warning about old format
if opt.oldfmt:
sys.stderr.write(
'Warning: The old format of the CPIN file can only be used for simulations with temp0=300.0!\n'
' You should use the new format for simulations with temperatures other than 300.0 Kelvins\n'
)
# Set the list of residue names we will be willing to titrate
titratable_residues = []
if notresnames is not None:
for resname in residues.titratable_residues:
if resname in notresnames: continue
titratable_residues.append(resname)
elif resnames is not None:
for resname in resnames:
if not resname in residues.titratable_residues:
raise AmberError('%s is not a titratable residue!' % resname)
elif not getattr(residues, resname).typ == "ph":
raise AmberError('%s is not a pH titratable residue!' %
resname)
titratable_residues.append(resname)
else:
for resname in residues.titratable_residues:
if getattr(residues, resname).typ == "ph":
titratable_residues.append(resname)
solvent_ions = [
'WAT', 'Na+', 'Br-', 'Cl-', 'Cs+', 'F-', 'I-', 'K+', 'Li+', 'Mg+',
'Rb+', 'CIO', 'IB', 'MG2'
]
# Filter titratable residues based on min and max pKa
new_reslist = []
for res in titratable_residues:
if getattr(residues, res).pKa < minpka: continue
if getattr(residues, res).pKa > maxpka: continue
new_reslist.append(res)
titratable_residues = new_reslist
del new_reslist
# Make sure we still have a couple residues
if len(titratable_residues) == 0:
raise AmberError('No titratable residues fit your criteria!')
# Load the topology file
parm = AmberParm(opt.prmtop)
# Replace an un-set notresnums with an empty list so we get __contains__()
if notresnums is None:
notresnums = []
# If we have a list of residue numbers, check that they're all titratable
if resnums is not None:
for resnum in resnums:
if resnum > parm.ptr('nres'):
raise AmberError('%s only has %d residues. (%d chosen)' %
(parm, parm.ptr('nres'), resnum))
if resnum <= 0:
raise AmberError('Cannot select negative residue numbers.')
resname = parm.parm_data['RESIDUE_LABEL'][resnum - 1]
if not resname in titratable_residues:
raise AmberError('Residue number %s [%s] is not titratable' %
(resnum, resname))
else:
# Select every residue except those in notresnums
resnums = []
for resnum in range(1, parm.ptr('nres') + 1):
if resnum in notresnums: continue
resnums.append(resnum)
solvated = False
first_solvent = 0
if 'WAT' in parm.parm_data['RESIDUE_LABEL']:
solvated = True
for i, res in enumerate(parm.parm_data['RESIDUE_LABEL']):
if res in solvent_ions:
first_solvent = parm.parm_data['RESIDUE_POINTER'][i]
break
main_reslist = TitratableResidueList(system_name=opt.system,
solvated=solvated,
first_solvent=first_solvent)
for resnum in resnums:
resname = parm.parm_data['RESIDUE_LABEL'][resnum - 1]
if not resname in titratable_residues: continue
res = getattr(residues, resname)
# Filter out termini (make sure the residue in the prmtop has as many
# atoms as the titratable residue defined in residues.py)
if resnum == parm.ptr('nres'):
natoms = (parm.ptr('natom') + 1 -
parm.parm_data['RESIDUE_POINTER'][resnum - 1])
else:
natoms = (parm.parm_data['RESIDUE_POINTER'][resnum] -
parm.parm_data['RESIDUE_POINTER'][resnum - 1])
if natoms != len(res.atom_list): continue
# If we have gotten this far, add it to the list.
main_reslist.add_residue(res, resnum,
parm.parm_data['RESIDUE_POINTER'][resnum - 1])
# Set the states if requested
if resstates is not None:
main_reslist.set_states(resstates)
# Open the output file
if opt.output is None:
output = sys.stdout
else:
output = open(opt.output, 'w')
main_reslist.write_cpin(output, opt.igb, opt.intdiel, opt.oldfmt, "ph")
if opt.output is not None:
output.close()
if solvated:
if opt.outparm is None:
has_carboxylate = False
for res in main_reslist:
if res is residues.AS4 or res is residues.GL4 or res is residues.PRN:
has_carboxylate = True
break
if has_carboxylate:
sys.stderr.write(
'Warning: Carboxylate residues in explicit solvent '
'simulations require a modified topology file!\n'
'Use the -op flag to print one.\n')
else:
changeRadii(parm, 'mbondi2').execute()
change(parm, 'RADII', ':AS4,GL4,PRN@OD=,OE=,O1=,O2=',
1.3).execute()
parm.overwrite = True
parm.write_parm(opt.outparm)
else:
if opt.outparm is not None:
sys.stderr.write(
'A new prmtop is only necessary for explicit solvent '
'CpHMD/pH-REMD simulations.\n')
sys.stderr.write('CPIN generation complete!\n')
def main(opt):
# Check all of the arguments
if not os.path.exists(opt.prmtop):
raise AmberError('prmtop file (%s) is missing' % opt.prmtop)
# Process the arguments that take multiple args
resstates = process_arglist(opt.resstates, int)
resnums = process_arglist(opt.resnums, int)
notresnums = process_arglist(opt.notresnums, int)
resnames = process_arglist(opt.resnames, str)
notresnames = process_arglist(opt.notresnames, str)
mineo = opt.mineo
maxeo = opt.maxeo
if not opt.igb in (1, 2, 5, 7, 8):
raise AmberError('-igb must be 1, 2, 5, 7, or 8!')
if resnums is not None and notresnums is not None:
raise AmberError('Cannot specify -resnums and -notresnums together')
if resnames is not None and notresnames is not None:
raise AmberError('Cannot specify -resnames and -notresnames together')
if opt.intdiel != 1 and opt.intdiel != 2:
raise AmberError('-intdiel must be either 1 or 2 currently')
# Set the list of residue names we will be willing to titrate
titratable_residues = []
if notresnames is not None:
for resname in residues.titratable_residues:
if resname in notresnames: continue
titratable_residues.append(resname)
elif resnames is not None:
for resname in resnames:
if not resname in residues.titratable_residues:
raise AmberError('%s is not a titratable residue!' % resname)
elif not getattr(residues, resname).typ == "redox":
raise AmberError(
'%s is not a redox-active titratable residue!' % resname)
titratable_residues.append(resname)
else:
for resname in residues.titratable_residues:
if getattr(residues, resname).typ == "redox":
titratable_residues.append(resname)
solvent_ions = [
'WAT', 'Na+', 'Br-', 'Cl-', 'Cs+', 'F-', 'I-', 'K+', 'Li+', 'Mg+',
'Rb+', 'CIO', 'IB', 'MG2'
]
# Filter titratable residues based on min and max pKa
new_reslist = []
for res in titratable_residues:
if getattr(residues, res).Eo < mineo: continue
if getattr(residues, res).Eo > maxeo: continue
new_reslist.append(res)
titratable_residues = new_reslist
del new_reslist
# Make sure we still have a couple residues
if len(titratable_residues) == 0:
raise AmberError('No titratable residues fit your criteria!')
# Load the topology file
parm = AmberParm(opt.prmtop)
# Replace an un-set notresnums with an empty list so we get __contains__()
if notresnums is None:
notresnums = []
# If we have a list of residue numbers, check that they're all titratable
if resnums is not None:
for resnum in resnums:
if resnum > parm.ptr('nres'):
raise AmberError('%s only has %d residues. (%d chosen)' %
(parm, parm.ptr('nres'), resnum))
if resnum <= 0:
raise AmberError('Cannot select negative residue numbers.')
resname = parm.parm_data['RESIDUE_LABEL'][resnum - 1]
if not resname in titratable_residues:
raise AmberError('Residue number %s [%s] is not titratable' %
(resnum, resname))
else:
# Select every residue except those in notresnums
resnums = []
for resnum in range(1, parm.ptr('nres') + 1):
if resnum in notresnums: continue
resnums.append(resnum)
solvated = False
first_solvent = 0
if 'WAT' in parm.parm_data['RESIDUE_LABEL']:
solvated = True
for i, res in enumerate(parm.parm_data['RESIDUE_LABEL']):
if res in solvent_ions:
first_solvent = parm.parm_data['RESIDUE_POINTER'][i]
break
main_reslist = TitratableResidueList(system_name=opt.system,
solvated=solvated,
first_solvent=first_solvent)
trescnt = 0
for resnum in resnums:
resname = parm.parm_data['RESIDUE_LABEL'][resnum - 1]
if not resname in titratable_residues: continue
res = getattr(residues, resname)
# Filter out termini (make sure the residue in the prmtop has as many
# atoms as the titratable residue defined in residues.py)
if resnum == parm.ptr('nres'):
natoms = (parm.ptr('natom') + 1 -
parm.parm_data['RESIDUE_POINTER'][resnum - 1])
else:
natoms = (parm.parm_data['RESIDUE_POINTER'][resnum] -
parm.parm_data['RESIDUE_POINTER'][resnum - 1])
if natoms != len(res.atom_list): continue
# If we have gotten this far, add it to the list.
main_reslist.add_residue(res, resnum,
parm.parm_data['RESIDUE_POINTER'][resnum - 1])
trescnt += 1
# Prints a warning if the number of titratable residues is larger than 50
if trescnt > 50:
sys.stderr.write(
'Warning: Your CEIN file has more than 50 titratable residues! pmemd and sander have a\n'
' default limit of 50 titrable residues, thus this CEIN file can only be used\n'
' if the definitions for this limit are modified at the top of\n'
' $AMBERHOME/src/pmemd/src/constante.F90 or $AMBERHOME/AmberTools/src/sander/constante.F90.\n'
' AMBER needs to be recompilied after these files are modified.\n'
)
# Set the states if requested
if resstates is not None:
main_reslist.set_states(resstates)
# Open the output file
if opt.output is None:
output = sys.stdout
else:
output = open(opt.output, 'w')
main_reslist.write_cpin(output, opt.igb, opt.intdiel, False, "redox")
if opt.output is not None:
output.close()
sys.stderr.write('CEIN generation complete!\n')
def main(opt):
# Check all of the arguments
if not os.path.exists(opt.prmtop):
raise AmberError('prmtop file (%s) is missing' % opt.prmtop)
# Process the arguments that take multiple args
resstates = process_arglist(opt.resstates, int)
resnums = process_arglist(opt.resnums, int)
notresnums = process_arglist(opt.notresnums, int)
resnames = process_arglist(opt.resnames, str)
notresnames = process_arglist(opt.notresnames, str)
minpka = opt.minpka
maxpka = opt.maxpka
if not opt.igb in (1, 2, 5, 7, 8):
raise AmberError('-igb must be 1, 2, 5, 7, or 8!')
if resnums is not None and notresnums is not None:
raise AmberError('Cannot specify -resnums and -notresnums together')
if resnames is not None and notresnames is not None:
raise AmberError('Cannot specify -resnames and -notresnames together')
if opt.intdiel != 1 and opt.intdiel != 2:
raise AmberError('-intdiel must be either 1 or 2 currently')
# Print warning about old format
if opt.oldfmt:
sys.stderr.write('Warning: The old format of the CPIN file can only be used for simulations with temp0=300.0!\n'
' You should use the new format for simulations with temperatures other than 300.0 Kelvins\n')
# Set the list of residue names we will be willing to titrate
titratable_residues = []
if notresnames is not None:
for resname in residues.titratable_residues:
if resname in notresnames: continue
titratable_residues.append(resname)
elif resnames is not None:
for resname in resnames:
if not resname in residues.titratable_residues:
raise AmberError('%s is not a titratable residue!' % resname)
elif not getattr(residues, resname).typ == "ph":
raise AmberError('%s is not a pH-active titratable residue!' % resname)
titratable_residues.append(resname)
else:
for resname in residues.titratable_residues:
if getattr(residues, resname).typ == "ph":
titratable_residues.append(resname)
solvent_ions = ['WAT', 'Na+', 'Br-', 'Cl-', 'Cs+', 'F-', 'I-', 'K+', 'Li+',
'Mg+', 'Rb+', 'CIO', 'IB', 'MG2']
# Filter titratable residues based on min and max pKa
new_reslist = []
for res in titratable_residues:
# @jaimergp: If None values are not filtered out, comparisons
# will fail in Py3k. This patch was discussed and approved in
# GitLab issue 122 (@vwcruzeiro, @swails)
# Error obtained in serial tests in conda-forge builds:
# Traceback (most recent call last):
# File "/home/conda/amber/bin/cpinutil.py", line 325, in <module>
# main(opt)
# File "/home/conda/amber/bin/cpinutil.py", line 191, in main
# if getattr(residues, res).pKa < minpka: continue
# TypeError: '<' not supported between instances of 'NoneType' and 'int'
# ./Run.cpin: Program error
# make[1]: *** [test.cpinutil] Error 1
if getattr(residues, res).pKa is None: continue
# /@jaimergp
if getattr(residues, res).pKa < minpka: continue
if getattr(residues, res).pKa > maxpka: continue
new_reslist.append(res)
titratable_residues = new_reslist
del new_reslist
# Make sure we still have a couple residues
if len(titratable_residues) == 0:
raise AmberError('No titratable residues fit your criteria!')
# Load the topology file
parm = AmberParm(opt.prmtop)
# Replace an un-set notresnums with an empty list so we get __contains__()
if notresnums is None:
notresnums = []
# If we have a list of residue numbers, check that they're all titratable
if resnums is not None:
for resnum in resnums:
if resnum > parm.ptr('nres'):
raise AmberError('%s only has %d residues. (%d chosen)' %
(parm, parm.ptr('nres'), resnum))
if resnum <= 0:
raise AmberError('Cannot select negative residue numbers.')
resname = parm.parm_data['RESIDUE_LABEL'][resnum-1]
if not resname in titratable_residues:
raise AmberError('Residue number %s [%s] is not titratable'
% (resnum, resname))
else:
# Select every residue except those in notresnums
resnums = []
for resnum in range(1, parm.ptr('nres') + 1):
if resnum in notresnums: continue
resnums.append(resnum)
solvated = False
first_solvent = 0
if 'WAT' in parm.parm_data['RESIDUE_LABEL']:
solvated = True
for i, res in enumerate(parm.parm_data['RESIDUE_LABEL']):
if res in solvent_ions:
first_solvent = parm.parm_data['RESIDUE_POINTER'][i]
break
main_reslist = TitratableResidueList(system_name=opt.system,
solvated=solvated, first_solvent=first_solvent)
trescnt = 0
for resnum in resnums:
resname = parm.parm_data['RESIDUE_LABEL'][resnum-1]
if not resname in titratable_residues: continue
res = getattr(residues, resname)
# Filter out termini (make sure the residue in the prmtop has as many
# atoms as the titratable residue defined in residues.py)
if resnum == parm.ptr('nres'):
natoms = (parm.ptr('natom') + 1 -
parm.parm_data['RESIDUE_POINTER'][resnum-1])
else:
natoms = (parm.parm_data['RESIDUE_POINTER'][resnum] -
parm.parm_data['RESIDUE_POINTER'][resnum-1])
if natoms != len(res.atom_list): continue
# If we have gotten this far, add it to the list.
main_reslist.add_residue(res, resnum,
parm.parm_data['RESIDUE_POINTER'][resnum-1])
trescnt += 1
# Prints a warning if the number of titratable residues is larger than 50
if trescnt > 50: sys.stderr.write('Warning: Your CPIN file has more than 50 titratable residues! pmemd and sander have a\n'
' default limit of 50 titrable residues, thus this CPIN file can only be used\n'
' if the definitions for this limit are modified at the top of\n'
' $AMBERHOME/src/pmemd/src/constantph.F90 or $AMBERHOME/AmberTools/src/sander/constantph.F90.\n'
' AMBER needs to be recompilied after these files are modified.\n')
# Set the states if requested
if resstates is not None:
main_reslist.set_states(resstates)
# Open the output file
if opt.output is None:
output = sys.stdout
else:
output = open(opt.output, 'w')
main_reslist.write_cpin(output, opt.igb, opt.intdiel, opt.oldfmt, "ph")
if opt.output is not None:
output.close()
if solvated:
if opt.outparm is None:
has_carboxylate = False
for res in main_reslist:
if res is residues.AS4 or res is residues.GL4 or res is residues.PRN:
has_carboxylate = True
break
if has_carboxylate:
sys.stderr.write(
'Warning: Carboxylate residues in explicit solvent '
'simulations require a modified topology file!\n'
' Use the -op flag to print one.\n'
)
else:
changeRadii(parm, 'mbondi2').execute()
change(parm, 'RADII', ':AS4,GL4,PRN@OD=,OE=,O1=,O2=', 1.3).execute()
parm.overwrite = True
parm.write_parm(opt.outparm)
else:
if opt.outparm is not None:
sys.stderr.write(
'A new prmtop is only necessary for explicit solvent '
'CpHMD/pH-REMD simulations.\n'
)
sys.stderr.write('CPIN generation complete!\n')
def main(opt):
# Check all of the arguments
if not os.path.exists(opt.prmtop):
raise AmberError('prmtop file (%s) is missing' % opt.prmtop)
# Process the arguments that take multiple args
resstates = process_arglist(opt.resstates, int)
resnums = process_arglist(opt.resnums, int)
notresnums = process_arglist(opt.notresnums, int)
resnames = process_arglist(opt.resnames, str)
notresnames = process_arglist(opt.notresnames, str)
minpka = opt.minpka
maxpka = opt.maxpka
if not opt.igb in (1, 2, 5, 7, 8):
raise AmberError('-igb must be 1, 2, 5, 7, or 8!')
if resnums is not None and notresnums is not None:
raise AmberError('Cannot specify -resnums and -notresnums together')
if resnames is not None and notresnames is not None:
raise AmberError('Cannot specify -resnames and -notresnames together')
if opt.intdiel != 1 and opt.intdiel != 2:
raise AmberError('-intdiel must be either 1 or 2 currently')
# Print warning about old format
if opt.oldfmt:
sys.stderr.write('Warning: The old format of the CPIN file can only be used for simulations with temp0=300.0!\n'
' You should use the new format for simulations with temperatures other than 300.0 Kelvins\n')
# Set the list of residue names we will be willing to titrate
titratable_residues = []
if notresnames is not None:
for resname in residues.titratable_residues:
if resname in notresnames: continue
titratable_residues.append(resname)
elif resnames is not None:
for resname in resnames:
if not resname in residues.titratable_residues:
raise AmberError('%s is not a titratable residue!' % resname)
elif not getattr(residues, resname).typ == "ph":
raise AmberError('%s is not a pH-active titratable residue!' % resname)
titratable_residues.append(resname)
else:
for resname in residues.titratable_residues:
if getattr(residues, resname).typ == "ph":
titratable_residues.append(resname)
solvent_ions = ['WAT', 'Na+', 'Br-', 'Cl-', 'Cs+', 'F-', 'I-', 'K+', 'Li+',
'Mg+', 'Rb+', 'CIO', 'IB', 'MG2']
# Filter titratable residues based on min and max pKa
new_reslist = []
for res in titratable_residues:
if getattr(residues, res).pKa < minpka: continue
if getattr(residues, res).pKa > maxpka: continue
new_reslist.append(res)
titratable_residues = new_reslist
del new_reslist
# Make sure we still have a couple residues
if len(titratable_residues) == 0:
raise AmberError('No titratable residues fit your criteria!')
# Load the topology file
parm = AmberParm(opt.prmtop)
# Replace an un-set notresnums with an empty list so we get __contains__()
if notresnums is None:
notresnums = []
# If we have a list of residue numbers, check that they're all titratable
if resnums is not None:
for resnum in resnums:
if resnum > parm.ptr('nres'):
raise AmberError('%s only has %d residues. (%d chosen)' %
(parm, parm.ptr('nres'), resnum))
if resnum <= 0:
raise AmberError('Cannot select negative residue numbers.')
resname = parm.parm_data['RESIDUE_LABEL'][resnum-1]
if not resname in titratable_residues:
raise AmberError('Residue number %s [%s] is not titratable'
% (resnum, resname))
else:
# Select every residue except those in notresnums
resnums = []
for resnum in range(1, parm.ptr('nres') + 1):
if resnum in notresnums: continue
resnums.append(resnum)
solvated = False
first_solvent = 0
if 'WAT' in parm.parm_data['RESIDUE_LABEL']:
solvated = True
for i, res in enumerate(parm.parm_data['RESIDUE_LABEL']):
if res in solvent_ions:
first_solvent = parm.parm_data['RESIDUE_POINTER'][i]
break
main_reslist = TitratableResidueList(system_name=opt.system,
solvated=solvated, first_solvent=first_solvent)
trescnt = 0
for resnum in resnums:
resname = parm.parm_data['RESIDUE_LABEL'][resnum-1]
if not resname in titratable_residues: continue
res = getattr(residues, resname)
# Filter out termini (make sure the residue in the prmtop has as many
# atoms as the titratable residue defined in residues.py)
if resnum == parm.ptr('nres'):
natoms = (parm.ptr('natom') + 1 -
parm.parm_data['RESIDUE_POINTER'][resnum-1])
else:
natoms = (parm.parm_data['RESIDUE_POINTER'][resnum] -
parm.parm_data['RESIDUE_POINTER'][resnum-1])
if natoms != len(res.atom_list): continue
# If we have gotten this far, add it to the list.
main_reslist.add_residue(res, resnum,
parm.parm_data['RESIDUE_POINTER'][resnum-1])
trescnt += 1
# Prints a warning if the number of titratable residues is larger than 50
if trescnt > 50: sys.stderr.write('Warning: Your CPIN file has more than 50 titratable residues! pmemd and sander have a\n'
' default limit of 50 titrable residues, thus this CPIN file can only be used\n'
' if the definitions for this limit are modified at the top of\n'
' $AMBERHOME/src/pmemd/src/constantph.F90 or $AMBERHOME/AmberTools/src/sander/constantph.F90.\n'
' AMBER needs to be recompilied after these files are modified.\n')
# Set the states if requested
if resstates is not None:
main_reslist.set_states(resstates)
# Open the output file
if opt.output is None:
output = sys.stdout
else:
output = open(opt.output, 'w')
main_reslist.write_cpin(output, opt.igb, opt.intdiel, opt.oldfmt, "ph")
if opt.output is not None:
output.close()
if solvated:
if opt.outparm is None:
has_carboxylate = False
for res in main_reslist:
if res is residues.AS4 or res is residues.GL4 or res is residues.PRN:
has_carboxylate = True
break
if has_carboxylate:
sys.stderr.write(
'Warning: Carboxylate residues in explicit solvent '
'simulations require a modified topology file!\n'
' Use the -op flag to print one.\n'
)
else:
changeRadii(parm, 'mbondi2').execute()
change(parm, 'RADII', ':AS4,GL4,PRN@OD=,OE=,O1=,O2=', 1.3).execute()
parm.overwrite = True
parm.write_parm(opt.outparm)
else:
if opt.outparm is not None:
sys.stderr.write(
'A new prmtop is only necessary for explicit solvent '
'CpHMD/pH-REMD simulations.\n'
)
sys.stderr.write('CPIN generation complete!\n')
class TestTrajRestartReporter(FileIOTestCase):
def setUp(self):
super().setUp()
self.amber_gas = AmberParm(self.get_fn('ash.parm7'),
self.get_fn('ash.rst7'))
def test_reporters(self):
""" Test NetCDF and ASCII restart and trajectory reporters (no PBC) """
with self.assertRaises(ValueError):
NetCDFReporter(self.get_fn('blah', written=True), 1, crds=False)
with self.assertRaises(ValueError):
MdcrdReporter(self.get_fn('blah', written=True), 1, crds=False)
with self.assertRaises(ValueError):
MdcrdReporter(self.get_fn('blah', written=True),
1,
crds=True,
vels=True)
system = self.amber_gas.createSystem()
integrator = mm.LangevinIntegrator(300 * u.kelvin, 5.0 / u.picoseconds,
1.0 * u.femtoseconds)
sim = app.Simulation(self.amber_gas.topology,
system,
integrator,
platform=CPU)
sim.context.setPositions(self.amber_gas.positions)
sim.reporters.extend([
NetCDFReporter(self.get_fn('traj1.nc', written=True), 10),
NetCDFReporter(self.get_fn('traj2.nc', written=True),
10,
vels=True),
NetCDFReporter(self.get_fn('traj3.nc', written=True),
10,
frcs=True),
NetCDFReporter(self.get_fn('traj4.nc', written=True),
10,
vels=True,
frcs=True),
NetCDFReporter(self.get_fn('traj5.nc', written=True),
10,
crds=False,
vels=True),
NetCDFReporter(self.get_fn('traj6.nc', written=True),
10,
crds=False,
frcs=True),
NetCDFReporter(self.get_fn('traj7.nc', written=True),
10,
crds=False,
vels=True,
frcs=True),
MdcrdReporter(self.get_fn('traj1.mdcrd', written=True), 10),
MdcrdReporter(self.get_fn('traj2.mdcrd', written=True),
10,
crds=False,
vels=True),
MdcrdReporter(self.get_fn('traj3.mdcrd', written=True),
10,
crds=False,
frcs=True),
RestartReporter(self.get_fn('restart.ncrst', written=True),
10,
write_multiple=True,
netcdf=True),
RestartReporter(self.get_fn('restart.rst7', written=True), 10),
])
sim.step(500)
for reporter in sim.reporters:
reporter.finalize()
self.assertEqual(len(os.listdir(self._temporary_directory.name)), 61)
ntraj = [
NetCDFTraj.open_old(self.get_fn('traj1.nc', written=True)),
NetCDFTraj.open_old(self.get_fn('traj2.nc', written=True)),
NetCDFTraj.open_old(self.get_fn('traj3.nc', written=True)),
NetCDFTraj.open_old(self.get_fn('traj4.nc', written=True)),
NetCDFTraj.open_old(self.get_fn('traj5.nc', written=True)),
NetCDFTraj.open_old(self.get_fn('traj6.nc', written=True)),
NetCDFTraj.open_old(self.get_fn('traj7.nc', written=True))
]
atraj = [
AmberMdcrd(self.get_fn('traj1.mdcrd', written=True),
self.amber_gas.ptr('natom'),
hasbox=False,
mode='r'),
AmberMdcrd(self.get_fn('traj2.mdcrd', written=True),
self.amber_gas.ptr('natom'),
hasbox=False,
mode='r'),
AmberMdcrd(self.get_fn('traj3.mdcrd', written=True),
self.amber_gas.ptr('natom'),
hasbox=False,
mode='r'),
]
for traj in ntraj:
self.assertEqual(traj.frame, 50)
self.assertEqual(traj.Conventions, 'AMBER')
self.assertEqual(traj.ConventionVersion, '1.0')
self.assertEqual(traj.application, 'AmberTools')
self.assertEqual(traj.program, 'ParmEd')
self.assertFalse(traj.hasbox)
self.assertTrue(ntraj[0].hascrds)
self.assertFalse(ntraj[0].hasvels)
self.assertFalse(ntraj[0].hasfrcs)
self.assertTrue(ntraj[1].hascrds)
self.assertTrue(ntraj[1].hasvels)
self.assertFalse(ntraj[1].hasfrcs)
self.assertTrue(ntraj[2].hascrds)
self.assertFalse(ntraj[2].hasvels)
self.assertTrue(ntraj[2].hasfrcs)
self.assertTrue(ntraj[3].hascrds)
self.assertTrue(ntraj[3].hasvels)
self.assertTrue(ntraj[3].hasfrcs)
self.assertFalse(ntraj[4].hascrds)
self.assertTrue(ntraj[4].hasvels)
self.assertFalse(ntraj[4].hasfrcs)
self.assertFalse(ntraj[5].hascrds)
self.assertFalse(ntraj[5].hasvels)
self.assertTrue(ntraj[5].hasfrcs)
self.assertFalse(ntraj[6].hascrds)
self.assertTrue(ntraj[6].hasvels)
self.assertTrue(ntraj[6].hasfrcs)
for i in (0, 2, 3, 4, 5, 6):
ntraj[i].close() # still need the 2nd
for traj in atraj:
traj.close()
# Now test the NetCDF restart files
fn = self.get_fn('restart.ncrst.%d', written=True)
for i, j in enumerate(range(10, 501, 10)):
ncrst = NetCDFRestart.open_old(fn % j)
self.assertEqual(ncrst.coordinates.shape, (1, 25, 3))
self.assertEqual(ncrst.velocities.shape, (1, 25, 3))
np.testing.assert_allclose(ncrst.coordinates[0],
ntraj[1].coordinates[i])
np.testing.assert_allclose(ncrst.velocities[0],
ntraj[1].velocities[i],
rtol=1e-6)
# Now test the ASCII restart file
f = AmberAsciiRestart(self.get_fn('restart.rst7', written=True), 'r')
# Compare to ncrst and make sure it's the same data
np.testing.assert_allclose(ncrst.coordinates, f.coordinates, atol=1e-3)
np.testing.assert_allclose(ncrst.velocities, f.velocities, rtol=1e-3)
# Make sure the EnergyMinimizerReporter does not fail
f = StringIO()
rep = EnergyMinimizerReporter(f)
rep.report(sim, frame=10)
rep.finalize()
@unittest.skipUnless(HAS_GROMACS, 'Cannot test without GROMACS')
def test_reporters_pbc(self):
""" Test NetCDF and ASCII restart and trajectory reporters (w/ PBC) """
systemsolv = load_file(self.get_fn('ildn.solv.top'),
xyz=self.get_fn('ildn.solv.gro'))
system = systemsolv.createSystem(nonbondedMethod=app.PME,
nonbondedCutoff=8 * u.angstroms)
integrator = mm.LangevinIntegrator(300 * u.kelvin, 5.0 / u.picoseconds,
1.0 * u.femtoseconds)
sim = app.Simulation(systemsolv.topology, system, integrator, CPU)
sim.context.setPositions(systemsolv.positions)
sim.reporters.extend([
NetCDFReporter(self.get_fn('traj.nc', written=True),
1,
vels=True,
frcs=True),
MdcrdReporter(self.get_fn('traj.mdcrd', written=True), 1),
RestartReporter(self.get_fn('restart.ncrst', written=True),
1,
netcdf=True),
RestartReporter(self.get_fn('restart.rst7', written=True), 1),
StateDataReporter(self.get_fn('state.o', written=True),
1,
volume=True,
density=True,
systemMass=1)
])
sim.step(5)
for reporter in sim.reporters:
reporter.finalize()
ntraj = NetCDFTraj.open_old(self.get_fn('traj.nc', written=True))
atraj = AmberMdcrd(self.get_fn('traj.mdcrd', written=True),
len(systemsolv.atoms),
True,
mode='r')
nrst = NetCDFRestart.open_old(
self.get_fn('restart.ncrst', written=True))
arst = AmberAsciiRestart(self.get_fn('restart.rst7', written=True),
'r')
self.assertEqual(ntraj.frame, 5)
self.assertEqual(atraj.frame, 5)
self.assertTrue(ntraj.hasvels)
self.assertTrue(ntraj.hasfrcs)
for i in range(ntraj.frame):
for x1, x2 in zip(ntraj.box[i], atraj.box[i]):
self.assertAlmostEqual(x1, x2, places=3)
self.assertEqual(len(nrst.box), 6)
self.assertEqual(len(arst.box), 6)
# Make sure the EnergyMinimizerReporter does not fail
f = StringIO()
rep = EnergyMinimizerReporter(f, volume=True)
rep.report(sim)
rep.finalize()
def test_private_functions(self):
""" Tests private helper functions for OMM reporters """
self.assertEqual(_format_time(7200), (2, 'hr.'))
self.assertEqual(_format_time(3600), (60, 'min.'))
self.assertEqual(_format_time(40), (40, 'sec.'))
def main(opt):
# Check all of the arguments
if not os.path.exists(opt.prmtop):
raise AmberError('prmtop file (%s) is missing' % opt.prmtop)
# Process the arguments that take multiple args
resstates = process_arglist(opt.resstates, int)
resnums = process_arglist(opt.resnums, int)
notresnums = process_arglist(opt.notresnums, int)
resnames = process_arglist(opt.resnames, str)
notresnames = process_arglist(opt.notresnames, str)
mineo = opt.mineo
maxeo = opt.maxeo
if not opt.igb in (1, 2, 5, 7, 8):
raise AmberError('-igb must be 1, 2, 5, 7, or 8!')
if resnums is not None and notresnums is not None:
raise AmberError('Cannot specify -resnums and -notresnums together')
if resnames is not None and notresnames is not None:
raise AmberError('Cannot specify -resnames and -notresnames together')
if opt.intdiel != 1 and opt.intdiel != 2:
raise AmberError('-intdiel must be either 1 or 2 currently')
# Set the list of residue names we will be willing to titrate
titratable_residues = []
if notresnames is not None:
for resname in residues.titratable_residues:
if resname in notresnames: continue
titratable_residues.append(resname)
elif resnames is not None:
for resname in resnames:
if not resname in residues.titratable_residues:
raise AmberError('%s is not a titratable residue!' % resname)
elif not getattr(residues, resname).typ == "redox":
raise AmberError('%s is not a redox-active titratable residue!' % resname)
titratable_residues.append(resname)
else:
for resname in residues.titratable_residues:
if getattr(residues, resname).typ == "redox":
titratable_residues.append(resname)
solvent_ions = ['WAT', 'Na+', 'Br-', 'Cl-', 'Cs+', 'F-', 'I-', 'K+', 'Li+',
'Mg+', 'Rb+', 'CIO', 'IB', 'MG2']
# Filter titratable residues based on min and max pKa
new_reslist = []
for res in titratable_residues:
if getattr(residues, res).Eo < mineo: continue
if getattr(residues, res).Eo > maxeo: continue
new_reslist.append(res)
titratable_residues = new_reslist
del new_reslist
# Make sure we still have a couple residues
if len(titratable_residues) == 0:
raise AmberError('No titratable residues fit your criteria!')
# Load the topology file
parm = AmberParm(opt.prmtop)
# Replace an un-set notresnums with an empty list so we get __contains__()
if notresnums is None:
notresnums = []
# If we have a list of residue numbers, check that they're all titratable
if resnums is not None:
for resnum in resnums:
if resnum > parm.ptr('nres'):
raise AmberError('%s only has %d residues. (%d chosen)' %
(parm, parm.ptr('nres'), resnum))
if resnum <= 0:
raise AmberError('Cannot select negative residue numbers.')
resname = parm.parm_data['RESIDUE_LABEL'][resnum-1]
if not resname in titratable_residues:
raise AmberError('Residue number %s [%s] is not titratable'
% (resnum, resname))
else:
# Select every residue except those in notresnums
resnums = []
for resnum in range(1, parm.ptr('nres') + 1):
if resnum in notresnums: continue
resnums.append(resnum)
solvated = False
first_solvent = 0
if 'WAT' in parm.parm_data['RESIDUE_LABEL']:
solvated = True
for i, res in enumerate(parm.parm_data['RESIDUE_LABEL']):
if res in solvent_ions:
first_solvent = parm.parm_data['RESIDUE_POINTER'][i]
break
main_reslist = TitratableResidueList(system_name=opt.system,
solvated=solvated, first_solvent=first_solvent)
trescnt = 0
for resnum in resnums:
resname = parm.parm_data['RESIDUE_LABEL'][resnum-1]
if not resname in titratable_residues: continue
res = getattr(residues, resname)
# Filter out termini (make sure the residue in the prmtop has as many
# atoms as the titratable residue defined in residues.py)
if resnum == parm.ptr('nres'):
natoms = (parm.ptr('natom') + 1 -
parm.parm_data['RESIDUE_POINTER'][resnum-1])
else:
natoms = (parm.parm_data['RESIDUE_POINTER'][resnum] -
parm.parm_data['RESIDUE_POINTER'][resnum-1])
if natoms != len(res.atom_list): continue
# If we have gotten this far, add it to the list.
main_reslist.add_residue(res, resnum,
parm.parm_data['RESIDUE_POINTER'][resnum-1])
trescnt += 1
# Prints a warning if the number of titratable residues is larger than 50
if trescnt > 50: sys.stderr.write('Warning: Your CEIN file has more than 50 titratable residues! pmemd and sander have a\n'
' default limit of 50 titrable residues, thus this CEIN file can only be used\n'
' if the definitions for this limit are modified at the top of\n'
' $AMBERHOME/src/pmemd/src/constante.F90 or $AMBERHOME/AmberTools/src/sander/constante.F90.\n'
' AMBER needs to be recompilied after these files are modified.\n')
# Set the states if requested
if resstates is not None:
main_reslist.set_states(resstates)
# Open the output file
if opt.output is None:
output = sys.stdout
else:
output = open(opt.output, 'w')
main_reslist.write_cpin(output, opt.igb, opt.intdiel, False, "redox")
if opt.output is not None:
output.close()
sys.stderr.write('CEIN generation complete!\n')
def main(opt):
# Check all of the arguments
if not os.path.exists(opt.prmtop):
raise AmberError('prmtop file (%s) is missing' % opt.prmtop)
# Process the arguments that take multiple args
resstates = process_arglist(opt.resstates, int)
resnums = process_arglist(opt.resnums, int)
notresnums = process_arglist(opt.notresnums, int)
resnames = process_arglist(opt.resnames, str)
notresnames = process_arglist(opt.notresnames, str)
minpka = opt.minpka
maxpka = opt.maxpka
if not opt.igb in (2, 5, 8):
raise AmberError('-igb must be 2, 5, or 8!')
if resnums is not None and notresnums is not None:
raise AmberError('Cannot specify -resnums and -notresnums together')
if resnames is not None and notresnames is not None:
raise AmberError('Cannot specify -resnames and -notresnames together')
if opt.intdiel != 1 and opt.intdiel != 2:
raise AmberError('-intdiel must be either 1 or 2 currently')
# Set the list of residue names we will be willing to titrate
titratable_residues = []
if notresnames is not None:
for resname in residues.titratable_residues:
if resname in notresnames: continue
titratable_residues.append(resname)
elif resnames is not None:
for resname in resnames:
if not resname in residues.titratable_residues:
raise AmberError('%s is not a titratable residue!' % resname)
titratable_residues.append(resname)
else:
titratable_residues = residues.titratable_residues[:]
solvent_ions = ['WAT', 'Na+', 'Br-', 'Cl-', 'Cs+', 'F-', 'I-', 'K+', 'Li+',
'Mg+', 'Rb+', 'CIO', 'IB', 'MG2']
# Filter titratable residues based on min and max pKa
new_reslist = []
for res in titratable_residues:
if getattr(residues, res).pKa < minpka: continue
if getattr(residues, res).pKa > maxpka: continue
new_reslist.append(res)
titratable_residues = new_reslist
del new_reslist
# Make sure we still have a couple residues
if len(titratable_residues) == 0:
raise AmberError('No titratable residues fit your criteria!')
# Load the topology file
parm = AmberParm(opt.prmtop)
# Replace an un-set notresnums with an empty list so we get __contains__()
if notresnums is None:
notresnums = []
# If we have a list of residue numbers, check that they're all titratable
if resnums is not None:
for resnum in resnums:
if resnum > parm.ptr('nres'):
raise AmberError('%s only has %d residues. (%d chosen)' %
(parm, parm.ptr('nres'), resnum))
if resnum <= 0:
raise AmberError('Cannot select negative residue numbers.')
resname = parm.parm_data['RESIDUE_LABEL'][resnum-1]
if not resname in titratable_residues:
raise AmberError('Residue number %s [%s] is not titratable'
% (resnum, resname))
else:
# Select every residue except those in notresnums
resnums = []
for resnum in range(1, parm.ptr('nres') + 1):
if resnum in notresnums: continue
resnums.append(resnum)
solvated = False
first_solvent = 0
if 'WAT' in parm.parm_data['RESIDUE_LABEL']:
solvated = True
for i, res in enumerate(parm.parm_data['RESIDUE_LABEL']):
if res in solvent_ions:
first_solvent = parm.parm_data['RESIDUE_POINTER'][i]
break
main_reslist = TitratableResidueList(system_name=opt.system,
solvated=solvated, first_solvent=first_solvent)
for resnum in resnums:
resname = parm.parm_data['RESIDUE_LABEL'][resnum-1]
if not resname in titratable_residues: continue
res = getattr(residues, resname)
# Filter out termini (make sure the residue in the prmtop has as many
# atoms as the titratable residue defined in residues.py)
if resnum == parm.ptr('nres'):
natoms = (parm.ptr('natom') + 1 -
parm.parm_data['RESIDUE_POINTER'][resnum-1])
else:
natoms = (parm.parm_data['RESIDUE_POINTER'][resnum] -
parm.parm_data['RESIDUE_POINTER'][resnum-1])
if natoms != len(res.atom_list): continue
# If we have gotten this far, add it to the list.
main_reslist.add_residue(res, resnum,
parm.parm_data['RESIDUE_POINTER'][resnum-1])
# Set the states if requested
if resstates is not None:
main_reslist.set_states(resstates)
# Open the output file
if opt.output is None:
output = sys.stdout
else:
output = open(opt.output, 'w')
main_reslist.write_cpin(output, opt.igb, opt.intdiel)
if opt.output is not None:
output.close()
if solvated:
if opt.outparm is None:
has_carboxylate = False
for res in main_reslist:
if res is residues.AS4 or res is residues.GL4:
has_carboxylate = True
break
if has_carboxylate:
sys.stderr.write(
'Warning: Carboxylate residues in explicit solvent '
'simulations require a modified topology file!\n'
'Use the -op flag to print one.\n'
)
else:
changeRadii(parm, 'mbondi2').execute()
change(parm, 'RADII', ':AS4,GL4@OD=,OE=', 1.3).execute()
parm.overwrite = True
parm.writeParm(opt.outparm)
else:
if opt.outparm is not None:
sys.stderr.write(
'A new prmtop is only necessary for explicit solvent '
'CpHMD/pH-REMD simulations.\n'
)
