Generate Hybrid Topology

Example on the use of pmx to prepare an hybrid topology. This is after running pdb2gmx on the mutant structure and obtaining a topology file from Gromacs.

The simplest case is the following (topol.top), where there are no itp files of other molecules included in the topology.

>>> from pmx.forcefield import Topology
>>> from pmx.alchemy import gen_hybrid_top

>>> # load the topology file
>>> top = Topology('topol.top')
>>> # fill B states for hybrid residues present
>>> pmxtop, _ = gen_hybrid_top(topol=top)
>>> # write topology to a new file
>>> pmxtop.write('pmxtop.top')

If the topology file includes different itp files (topol2.top, topol2.itp), these too can be modified and returned by setting the recursive argument to True.

>>> # load the topology file
>>> top = Topology('topol2.top')
>>> # fill B states for hybrid residues present in topol2.itp
>>> pmxtop, pmxitps = gen_hybrid_top(topol=top, recursive=True)
>>> # write topology and itps to a new file
>>> pmxtop.write('pmxtop.top')
>>> for i, itp in enumerate(pmxitps):
>>>     itp.write(itp.filename)

The above will overwrite the original itp files. If you want to save the new pmx itp file without losing the original files, you can do as follows:

>>> for i, itp in enumerate(pmxitps):
>>>     itp.write('pmxitp_%s.itp' % i)

You will then need to update the pmxtop.top accordingly so to include the new itp file.

If you like getting lots of screen output, you can set the verbose argument to True.

>>> pmxtop, pmxitps = gen_hybrid_top(topol=top, recursive=True, verbose=True)
log_> Reading input top file "topol2.top"
log_> Making bonds for state B -> 0 bonds with perturbed atoms
log_> Making angles for state B -> 0 angles with perturbed atoms
log_> Making dihedrals for state B -> 0 dihedrals with perturbed atoms
log_> Removed 0 fake dihedrals
log_> Total charge of state A = 0
log_> Total charge of state B = 0

log_> Reading input itp file "topol2.itp""
log_> Scanning database for D2A
log_> Scanning database for G2R
log_> Scanning database for P2A
log_> Hybrid Residue -> 9 | D2A
log_> Hybrid Residue -> 10 | G2R
log_> Hybrid Residue -> 12 | P2A
log_> Making bonds for state B -> 61 bonds with perturbed atoms
log_> Making angles for state B -> 127 angles with perturbed atoms
log_> Making dihedrals for state B -> 190 dihedrals with perturbed atoms
log_> Removed 19 fake dihedrals
log_> Total charge of state A = 1
log_> Total charge of state B = 3