[gmx-users] Topology for Cross linked polymer chains

[Justin Lemkul]

On 3/27/15 9:25 AM, sridhar dwadasi wrote:
> 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:
> """
> GROMACS is written by:
> Emile Apol         Rossen Apostolov   Herman J.C. Berendsen Par
> Bjelkmar
> 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
> Peter Tieleman     Christian Wennberg Maarten Wolf
> and the project leaders:
> Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel
>
> Copyright (c) 1991-2000, University of Groningen, The Netherlands.
> Copyright (c) 2001-2014, The GROMACS development team at
> Uppsala University, Stockholm University and
> the Royal Institute of Technology, Sweden.
> check out http://www.gromacs.org for more information.
>
> GROMACS is free software; you can redistribute it and/or modify it
> under the terms of the GNU Lesser General Public License
> as published by the Free Software Foundation; either version 2.1
> of the License, or (at your option) any later version.
>
> 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?

Yes.

> Also in many posts I have seen that even if it generates topology, the
> generated topology must be carefully checked. Is it system dependent?
>

Any method that is guessing atom types, charges, etc. from a database of generic 
parameters needs to be checked.  These are not predefined, optimized parameters 
like one would find in an .rtp file from a thoroughly parametrized force field.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==================================================