def __init__(self,
amber_sys,
num_steps=1000,
igb=5,
restrained=True,
rst_wt=10.0,
rst_mask='@CA,C,O,N'):
""" Sets up a minimization input file """
# Type checking
if type(num_steps).__name__ != 'int':
raise TypeError('num_steps must be an integer!')
if type(igb).__name__ != 'int':
raise TypeError('igb must be an integer!')
# Create the mdin instance
self.mdin = mdin(self.program)
# Set up periodic/non-periodic settings
if amber_sys.periodic():
self.mdin.change('cntrl', 'ntb', 1)
else:
self.mdin.change('cntrl', 'ntb', 0)
if not igb in [1, 2, 5, 7, 8]:
raise ValueError('For non-periodic systems, igb must be ' +
'1, 2, 5, 7, or 8')
self.mdin.change('cntrl', 'igb', igb)
self.mdin.change('cntrl', 'cut', 1000.0)
self.mdin.change('cntrl', 'imin', 1)
self.mdin.change('cntrl', 'maxcyc', num_steps)
self.mdin.change('cntrl', 'ntr', int(restrained))
if restrained:
self.mdin.change('cntrl', 'restraint_wt', rst_wt)
self.mdin.change('cntrl', 'restraintmask', rst_mask)
def __init__(self, amber_sys, num_steps=1000, igb=5, restrained=True,
rst_wt=10.0, rst_mask='@CA,C,O,N'):
""" Sets up a minimization input file """
# Type checking
if type(num_steps).__name__ != 'int':
raise TypeError('num_steps must be an integer!')
if type(igb).__name__ != 'int':
raise TypeError('igb must be an integer!')
# Create the mdin instance
self.mdin = mdin(self.program)
# Set up periodic/non-periodic settings
if amber_sys.periodic():
self.mdin.change('cntrl', 'ntb', 1)
else:
self.mdin.change('cntrl', 'ntb', 0)
if not igb in [1, 2, 5, 7, 8]:
raise ValueError('For non-periodic systems, igb must be ' +
'1, 2, 5, 7, or 8')
self.mdin.change('cntrl', 'igb', igb)
self.mdin.change('cntrl', 'cut', 1000.0)
self.mdin.change('cntrl', 'imin', 1)
self.mdin.change('cntrl', 'maxcyc', num_steps)
self.mdin.change('cntrl', 'ntr', int(restrained))
if restrained:
self.mdin.change('cntrl', 'restraint_wt', rst_wt)
self.mdin.change('cntrl', 'restraintmask', rst_mask)
def __init__(self, amber_sys, nstlim=1000, igb=5, restrained=False,
rst_wt=2.0, rst_mask='@CA,C,O,N', temp0=300.0,
thermostat='langevin', thermostat_param=5.0, barostat=None,
barostat_param=5.0, ntpr=1000, ntwr=10000, ntwx=1000,
restart=True, dt=0.002):
# Create the mdin instance
self.mdin = mdin(self.program)
# Do we have velocities?
if restart:
self.mdin.change('cntrl', 'ntx', 5)
self.mdin.change('cntrl', 'irest', 1)
# Set up periodic/non-periodic settings
if amber_sys.periodic():
if barostat.lower() == 'berendsen':
self.mdin.change('cntrl', 'ntb', 2)
self.mdin.change('cntrl', 'ntp', 1)
self.mdin.change('cntrl', 'taup', barostat_param)
elif barostat.lower() == 'none':
pass
elif barostat:
raise ValueError('barostat must be "berendsen" or None/False')
else:
self.mdin.change('cntrl', 'ntb', 1)
else:
# Type-check igb
if type(igb).__name__ != 'int':
raise TypeError('igb must be an integer!')
self.mdin.change('cntrl', 'ntb', 0)
if not igb in [1, 2, 5, 7, 8]:
raise ValueError('For non-periodic systems, igb must be ' +
'1, 2, 5, 7, or 8')
self.mdin.change('cntrl', 'igb', igb)
self.mdin.change('cntrl', 'cut', 1000.0)
self.mdin.change('cntrl', 'ioutfm', 1) # always NetCDF!
self.mdin.change('cntrl', 'ntr', int(restrained))
self.mdin.change('cntrl', 'ig', -1)
self.mdin.change('cntrl', 'ntc', 2)
self.mdin.change('cntrl', 'ntf', 2)
self.mdin.change('cntrl', 'ntpr', ntpr)
self.mdin.change('cntrl', 'ntwx', ntwx)
self.mdin.change('cntrl', 'ntwr', ntwr)
self.mdin.change('cntrl', 'nstlim', nstlim)
self.mdin.change('cntrl', 'dt', dt)
if thermostat.lower() == 'langevin':
self.mdin.change('cntrl', 'ntt', 3)
self.mdin.change('cntrl', 'gamma_ln', thermostat_param)
elif thermostat.lower() == 'berendsen':
self.mdin.change('cntrl', 'ntt', 1)
self.mdin.change('cntrl', 'tautp', thermostat_param)
else:
raise ValueError('thermostat must be langevin or berendsen!')
if restrained:
self.mdin.change('cntrl', 'restraint_wt', rst_wt)
self.mdin.change('cntrl', 'restraintmask', rst_mask)
def __init__(self, amber_sys, nstlim=1000, igb=5, restrained=True,
rst_wt=2.0, rst_mask='@CA,C,O,N', temp0=300.0, tempi=10.0,
slow=False, thermostat='langevin', thermostat_param=5.0,
ntpr=1000, ntwx=1000, ntwr=10000, dt=0.002):
""" Sets up a heating input file """
# Type checking
if type(nstlim).__name__ != 'int':
raise TypeError('nstlim must be an integer!')
# Create the mdin instance
self.mdin = mdin(self.program)
# Set up periodic/non-periodic settings
if amber_sys.periodic():
self.mdin.change('cntrl', 'ntb', 1)
else:
# Type-check igb
if type(igb).__name__ != 'int':
raise TypeError('igb must be an integer!')
self.mdin.change('cntrl', 'ntb', 0)
if not igb in [1, 2, 5, 7, 8]:
raise ValueError('For non-periodic systems, igb must be ' +
'1, 2, 5, 7, or 8')
self.mdin.change('cntrl', 'igb', igb)
self.mdin.change('cntrl', 'cut', 1000.0)
self.mdin.change('cntrl', 'ioutfm', 1) # always NetCDF!
if not slow: self.mdin.change('cntrl', 'tempi', tempi)
self.mdin.change('cntrl', 'temp0', temp0)
self.mdin.change('cntrl', 'ntr', int(restrained))
self.mdin.change('cntrl', 'ig', -1)
self.mdin.change('cntrl', 'ntc', 2)
self.mdin.change('cntrl', 'ntf', 2)
self.mdin.change('cntrl', 'ntpr', ntpr)
self.mdin.change('cntrl', 'ntwx', ntwx)
self.mdin.change('cntrl', 'ntwr', ntwr)
self.mdin.change('cntrl', 'nstlim', nstlim)
self.mdin.change('cntrl', 'dt', dt)
if thermostat.lower() == 'langevin':
self.mdin.change('cntrl', 'ntt', 3)
self.mdin.change('cntrl', 'gamma_ln', thermostat_param)
elif thermostat.lower() == 'berendsen':
self.mdin.change('cntrl', 'ntt', 1)
self.mdin.change('cntrl', 'tautp', thermostat_param)
else:
raise ValueError('thermostat must be langevin or berendsen!')
if restrained:
self.mdin.change('cntrl', 'restraint_wt', rst_wt)
self.mdin.change('cntrl', 'restraintmask', rst_mask)
if slow:
self.mdin.add_lines("&wt\n TYPE='TEMP0', ISTEP1=0, ISTEP2=%d" %
((nstlim * 2) // 3))
self.mdin.add_lines((" VALUE1=%.2f, VALUE2=%.2f,\n/\n" +
"&wt TYPE='END' /") % (tempi, temp0))
print >> sys.stderr, 'Error: Unrecognized input option %s!' % sys.argv[
i]
usage()
i += 1
except IndexError:
print >> sys.stderr, 'Error: Expecting more command line arguments!'
usage()
except ValueError:
print >> sys.stderr, 'Error: Unexpected data types obtained (i.e. float, int, etc.)'
usage()
FACTOR *= pH # put the pH in the factor
# Variable declaration
pmemd_input = mdin('pmemd') # we're creating a pmemd input file
pmemd_energy = mdin('pmemd') # we're creating another pmemd input file
parm = amberParm(prmtop)
resstates = []
chrgdat = []
protcnt = []
num_states = []
first_state = []
first_charge = []
first_atom = []
num_atoms = []
statene = []
trescnt = 0
# Check for errors and parse CPIN file.
if not parm.exists:
def __init__(self,
amber_sys,
nstlim=1000,
igb=5,
restrained=False,
rst_wt=2.0,
rst_mask='@CA,C,O,N',
temp0=300.0,
thermostat='langevin',
thermostat_param=5.0,
barostat=None,
barostat_param=5.0,
ntpr=1000,
ntwr=10000,
ntwx=1000,
restart=True,
dt=0.002):
# Create the mdin instance
self.mdin = mdin(self.program)
# Do we have velocities?
if restart:
self.mdin.change('cntrl', 'ntx', 5)
self.mdin.change('cntrl', 'irest', 1)
# Set up periodic/non-periodic settings
if amber_sys.periodic():
if barostat.lower() == 'berendsen':
self.mdin.change('cntrl', 'ntb', 2)
self.mdin.change('cntrl', 'ntp', 1)
self.mdin.change('cntrl', 'taup', barostat_param)
elif barostat.lower() == 'none':
pass
elif barostat:
raise ValueError('barostat must be "berendsen" or None/False')
else:
self.mdin.change('cntrl', 'ntb', 1)
else:
# Type-check igb
if type(igb).__name__ != 'int':
raise TypeError('igb must be an integer!')
self.mdin.change('cntrl', 'ntb', 0)
if not igb in [1, 2, 5, 7, 8]:
raise ValueError('For non-periodic systems, igb must be ' +
'1, 2, 5, 7, or 8')
self.mdin.change('cntrl', 'igb', igb)
self.mdin.change('cntrl', 'cut', 1000.0)
self.mdin.change('cntrl', 'ioutfm', 1) # always NetCDF!
self.mdin.change('cntrl', 'ntr', int(restrained))
self.mdin.change('cntrl', 'ig', -1)
self.mdin.change('cntrl', 'ntc', 2)
self.mdin.change('cntrl', 'ntf', 2)
self.mdin.change('cntrl', 'ntpr', ntpr)
self.mdin.change('cntrl', 'ntwx', ntwx)
self.mdin.change('cntrl', 'ntwr', ntwr)
self.mdin.change('cntrl', 'nstlim', nstlim)
self.mdin.change('cntrl', 'dt', dt)
if thermostat.lower() == 'langevin':
self.mdin.change('cntrl', 'ntt', 3)
self.mdin.change('cntrl', 'gamma_ln', thermostat_param)
elif thermostat.lower() == 'berendsen':
self.mdin.change('cntrl', 'ntt', 1)
self.mdin.change('cntrl', 'tautp', thermostat_param)
else:
raise ValueError('thermostat must be langevin or berendsen!')
if restrained:
self.mdin.change('cntrl', 'restraint_wt', rst_wt)
self.mdin.change('cntrl', 'restraintmask', rst_mask)
def __init__(self,
amber_sys,
nstlim=1000,
igb=5,
restrained=True,
rst_wt=2.0,
rst_mask='@CA,C,O,N',
temp0=300.0,
tempi=10.0,
slow=False,
thermostat='langevin',
thermostat_param=5.0,
ntpr=1000,
ntwx=1000,
ntwr=10000,
dt=0.002):
""" Sets up a heating input file """
# Type checking
if type(nstlim).__name__ != 'int':
raise TypeError('nstlim must be an integer!')
# Create the mdin instance
self.mdin = mdin(self.program)
# Set up periodic/non-periodic settings
if amber_sys.periodic():
self.mdin.change('cntrl', 'ntb', 1)
else:
# Type-check igb
if type(igb).__name__ != 'int':
raise TypeError('igb must be an integer!')
self.mdin.change('cntrl', 'ntb', 0)
if not igb in [1, 2, 5, 7, 8]:
raise ValueError('For non-periodic systems, igb must be ' +
'1, 2, 5, 7, or 8')
self.mdin.change('cntrl', 'igb', igb)
self.mdin.change('cntrl', 'cut', 1000.0)
self.mdin.change('cntrl', 'ioutfm', 1) # always NetCDF!
if not slow: self.mdin.change('cntrl', 'tempi', tempi)
self.mdin.change('cntrl', 'temp0', temp0)
self.mdin.change('cntrl', 'ntr', int(restrained))
self.mdin.change('cntrl', 'ig', -1)
self.mdin.change('cntrl', 'ntc', 2)
self.mdin.change('cntrl', 'ntf', 2)
self.mdin.change('cntrl', 'ntpr', ntpr)
self.mdin.change('cntrl', 'ntwx', ntwx)
self.mdin.change('cntrl', 'ntwr', ntwr)
self.mdin.change('cntrl', 'nstlim', nstlim)
self.mdin.change('cntrl', 'dt', dt)
if thermostat.lower() == 'langevin':
self.mdin.change('cntrl', 'ntt', 3)
self.mdin.change('cntrl', 'gamma_ln', thermostat_param)
elif thermostat.lower() == 'berendsen':
self.mdin.change('cntrl', 'ntt', 1)
self.mdin.change('cntrl', 'tautp', thermostat_param)
else:
raise ValueError('thermostat must be langevin or berendsen!')
if restrained:
self.mdin.change('cntrl', 'restraint_wt', rst_wt)
self.mdin.change('cntrl', 'restraintmask', rst_mask)
if slow:
self.mdin.add_lines("&wt\n TYPE='TEMP0', ISTEP1=0, ISTEP2=%d" %
((nstlim * 2) // 3))
self.mdin.add_lines(
(" VALUE1=%.2f, VALUE2=%.2f,\n/\n" + "&wt TYPE='END' /") %
(tempi, temp0))
script = open(scriptname, 'w')
break
except IOError:
print "Could not open file", scriptname, "for writing."
sys.stdout.write("Alternative script file name: ")
scriptname = sys.stdin.readline().rstrip('\r\n')
# Print out the shebang.
script.write("#!/bin/sh\n\n")
query_parallel()
# Close the script file and give it rwxr-xr-x permissions
script.close()
os.chmod(scriptname, 0755)
# Create a new mdin object appropriate for sander
mdin_contents = mdin("sander")
# Set the mdin simulation title
sys.stdout.write("Simulation title: ")
mdin_contents.title = sys.stdin.readline().rstrip('\r\n')
# Write the mdin file
mdin_contents.write(mdin_name)
# End the program
finished()
