[gmx-users] Branched topology / Converting from psf

Roland Schulz roland at utk.edu
Sun Jan 25 01:36:57 CET 2009


is there a smart way to build the topology (topol.top) for a branched
polymer? In this case I try to build Lignin. The problem is that I need to
apply a patch to each monomer depending on the connection and (as far as I
understand) the termini databases are only applied to the end of a chain.
Also I think the termini database is the only watch to apply a patch in the
sense of changing charges. Any recommendation for a good tool or a way to do
it with pdb2gmx would be very helpful.
I have a psf topology. Has someone a script to convert a psf topology to a
gromacs topology?


ORNL/UT Center for Molecular Biophysics cmb.ornl.gov
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