6.1. ligandparam.multiresp.mdinutils

This code is used to generate input files for AMBER simulations.

The main classes are: - AmberCmd: used to generate the command line for sander.MPI - Mdin: used to generate the mdin file - Disang1D: used to generate the disang file for distance restraints - Disang2D: used to generate the disang file for distance restraints - Computer: used to generate the bash script for running the simulation - BASH: used to generate the bash script for running the simulation - PERCEVAL: used to generate the bash script for running the simulation

This code was initially developed by Prof. Timothy Giese at Rutgers University, and was reproduced more or less in its entirety here (with modifications to the code for readibility and documentation).

class ligandparam.multiresp.mdinutils.AmberCmd(base=None, inpcrd=None)[source]

Bases: object

This class is used to generate the command line for sander.MPI

Attributes:

dipout
mdfrc

Methods

`CmdString`()	Generate the command line string for sander.MPI
`SetBaseName`(base)	Set the base name of the simulation.
`SetDefaults`()	Set the default values for the AmberCmd object.
`SetGroupSize`(gsize[, gmmsize])	Set the group size.

Initialize the AmberCmd object.

Parameters:

base (str, optional) – The base name of the simulation
inpcrd (str, optional) – The name of the inpcrd file

Attributes:

dipout
mdfrc

Methods

`CmdString`()	Generate the command line string for sander.MPI
`SetBaseName`(base)	Set the base name of the simulation.
`SetDefaults`()	Set the default values for the AmberCmd object.
`SetGroupSize`(gsize[, gmmsize])	Set the group size.

CmdString()[source]: Generate the command line string for sander.MPI

SetBaseName(base)[source]: Set the base name of the simulation.

SetDefaults()[source]: Set the default values for the AmberCmd object.

SetGroupSize(gsize, gmmsize=None)[source]

Set the group size.

Parameters:

gsize (int) – The group size
gmmsize (int, optional) – The gmm size

crd7 = 'inpcrd'

dipout = None

exe = '${AMBERHOME}/bin/sander.MPI'

mdfrc = None

mdin = 'mdin'

mdinfo = 'mdinfo'

mdout = 'mdout'

nc = 'mdcrd'

parm7 = 'prmtop'

refc = 'refc'

rst7 = 'restrt'

class ligandparam.multiresp.mdinutils.Disang1D(template, r1, k1)[source]

Bases: object

This class is used to generate the disang file for distance restraints.

Methods

WriteDisang(fname)

Write the disang file.

Initialize the Disang1D object.

Parameters:

template (str) – The template file
r1 (float) – The distance restraint
k1 (float) – The force constant

Methods

WriteDisang(fname)

Write the disang file.

WriteDisang(fname)[source]

Write the disang file.

Parameters:: fname (str) – The name of the file

class ligandparam.multiresp.mdinutils.Disang2D(template, r1, k1, r2, k2)[source]

Bases: object

This class is used to generate the disang file for distance restraints.

Methods

WriteDisang(fname)

Write the disang file.

Initialize the Disang2D object.

Parameters:

template (str) – The template file
r1 (float) – The distance restraint for the first atom
k1 (float) – The force constant for the first atom
r2 (float) – The distance restraint for the second atom
k2 (float) – The force constant for the second atom

Methods

WriteDisang(fname)

Write the disang file.

WriteDisang(fname)[source]

Write the disang file.

Parameters:: fname (str) – The name of the file

class ligandparam.multiresp.mdinutils.Mdin(base=None, inpcrd=None)[source]

Bases: AmberCmd

This class is used to generate the mdin file.

Attributes:

dipout
mdfrc

Methods

`Add_TempChange`(time0, time1, temp0, temp1)	Add a temperature change.
`CmdString`()	Generate the command line string for sander.MPI
`SetBaseName`(base)	Set the base name of the simulation.
`SetDefaults`()	Set the default values for the AmberCmd object.
`SetGroupSize`(gsize[, gmmsize])	Set the group size.
`Set_DLFIND`([active])	Set the DLFind.
`Set_DLFIND_Minimize`()	Set the DLFind minimization.
`Set_DLFIND_TransitionState`(displaced_rst7)	Set the DLFind transition state.
`Set_DumpFreq`(dumpfreq)	Set the dump frequency.
`Set_NPT`([temp0])	Set the NPT ensemble.
`Set_NVE`()	Set the NVE ensemble.
`Set_NVT`([temp0])	Set the NVT ensemble.
`Set_PrintFreq`(freq)	Set the print frequency.
`Set_QMMM_AM1`([qmmask, qmcharge, tight])	Set the QMMM AM1 method.
`Set_QMMM_PBE0`([qmmask, qmcharge, basis, tight])	Set the QMMM PBE0 method.
`Set_Restart`([restart])	Set the restart.
`WriteMdin`([directory])	Write the mdin file.

Initialize the Mdin object.

Parameters:

base (str, optional) – The base name of the simulation
inpcrd (str, optional) – The name of the inpcrd file

Attributes:

dipout
mdfrc

Methods

`Add_TempChange`(time0, time1, temp0, temp1)	Add a temperature change.
`CmdString`()	Generate the command line string for sander.MPI
`SetBaseName`(base)	Set the base name of the simulation.
`SetDefaults`()	Set the default values for the AmberCmd object.
`SetGroupSize`(gsize[, gmmsize])	Set the group size.
`Set_DLFIND`([active])	Set the DLFind.
`Set_DLFIND_Minimize`()	Set the DLFind minimization.
`Set_DLFIND_TransitionState`(displaced_rst7)	Set the DLFind transition state.
`Set_DumpFreq`(dumpfreq)	Set the dump frequency.
`Set_NPT`([temp0])	Set the NPT ensemble.
`Set_NVE`()	Set the NVE ensemble.
`Set_NVT`([temp0])	Set the NVT ensemble.
`Set_PrintFreq`(freq)	Set the print frequency.
`Set_QMMM_AM1`([qmmask, qmcharge, tight])	Set the QMMM AM1 method.
`Set_QMMM_PBE0`([qmmask, qmcharge, basis, tight])	Set the QMMM PBE0 method.
`Set_Restart`([restart])	Set the restart.
`WriteMdin`([directory])	Write the mdin file.

Add_TempChange(time0, time1, temp0, temp1)[source]

Add a temperature change.

Parameters:

time0 (int) – The initial time
time1 (int) – The final time
temp0 (float) – The initial temperature
temp1 (float) – The final temperature

Set_DLFIND(active=None)[source]

Set the DLFind.

Parameters:: active (str, optional) – The active atoms. Default is None

Set_DLFIND_Minimize()[source]: Set the DLFind minimization.

Set_DLFIND_TransitionState(displaced_rst7)[source]

Set the DLFind transition state.

Parameters:: displaced_rst7 (str) – The name of the displaced restart file

Set_DumpFreq(dumpfreq)[source]

Set the dump frequency.

Parameters:: dumpfreq (int) – The dump frequency

Set_NPT(temp0=298.0)[source]

Set the NPT ensemble.

Parameters:: temp0 (float, optional) – The initial temperature. Default is 298.0

Set_NVE()[source]: Set the NVE ensemble.

Set_NVT(temp0=298.0)[source]

Set the NVT ensemble.

Parameters:: temp0 (float, optional) – The initial temperature. Default is 298.0

Set_PrintFreq(freq)[source]

Set the print frequency.

Parameters:: freq (int) – The print frequency

Set_QMMM_AM1(qmmask=None, qmcharge=None, tight=False)[source]

Set the QMMM AM1 method.

Parameters:

qmmask (str, optional) – The quantum mask. Default is None
qmcharge (int, optional) – The quantum charge. Default is None
tight (bool, optional) – If True, the simulation will be tight. Default is False

Set_QMMM_PBE0(qmmask=None, qmcharge=None, basis=None, tight=False)[source]

Set the QMMM PBE0 method.

Parameters:

qmmask (str, optional) – The quantum mask. Default is None
qmcharge (int, optional) – The quantum charge. Default is None
basis (str, optional) – The basis set. Default is None
tight (bool, optional) – If True, the simulation will be tight. Default is False

Set_Restart(restart=True)[source]

Set the restart.

Parameters:: restart (bool, optional) – If True, the simulation will be restarted. Default is True

WriteMdin(directory=None)[source]

Write the mdin file.

Parameters:: directory (str, optional) – The directory where the mdin file will be written. Default is None