[gmx-users] Topology for Cross linked polymer chains

[sridhar dwadasi]

Hi Justin Lemkul,
                 Thank you very much for the reply. I have tried using
x2top for generating topology. I copied contents of opls ff to poly ff and
added some atoms and ran the command. The output was as follows:
"""
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Aldert van Buuren  Rudi van Drunen    Anton Feenstra     Sebastian Fritsch
Gerrit Groenhof    Christoph Junghans Peter Kasson       Carsten Kutzner
Per Larsson        Justin A. Lemkul   Magnus Lundborg    Pieter Meulenhoff
Erik Marklund      Teemu Murtola      Szilard Pall       Sander Pronk
Roland Schulz      Alexey Shvetsov    Michael Shirts     Alfons Sijbers
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and the project leaders:
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GROMACS:      gmx x2top, VERSION 5.0.2
Executable:   /usr/local/gromacs/bin/gmx
Library dir:  /usr/local/gromacs/share/gromacs/top
Command line:
  gmx x2top -f polyngta_nm.pdb -ff poly -o check.rtp -v -param

Opening force field file ./poly.ff/atomname2type.n2t
There are 9 name to type translations in file ./poly.ff
Generating bonds from distances...
atom 162
There are 7 different atom types in your sample
Generating angles and dihedrals from bonds...
Segmentation fault (core dumped)

"""
It returned an error. I have seen posts earlier regarding an error in the
code in version 5. Is it related to that?
Also in many posts I have seen that even if it generates topology, the
generated topology must be carefully checked. Is it system dependent?

Thank You
Sridhar