[gmx-users] Reg: Prodrg topology

Mark Abraham mark.abraham at anu.edu.au
Tue Oct 5 08:00:02 CEST 2010

Pre-supposing the suitability of only one tool is pretty limiting - and that's before you consider the weaknesses of PRODRG even for its target forcefields.

For decane, writing the topology by hand is feasible. There's at most 3 atom types and only 32 atoms, after all. Otherwise, consider http://www.gromacs.org/index.php?title=Download_%26_Installation/Related_Software/MKTOP

----- Original Message -----
From: vinothkumar mohanakrishnan <kmvinoth at gmail.com>
Date: Tuesday, October 5, 2010 16:43
Subject: [gmx-users] Reg: Prodrg topology
To: Discussion list for GROMACS users <gmx-users at gromacs.org>

> Hi all
> I want to generate a topology file for say decane from prodrg for oplsaa force field. is it possible?. i get a topology file from prodrg for gromos96.1 force field and i am able to process it further. when i use the topology file generated for gromos96.1(from prodrg) for oplsaa i get the error (during grompp) as atomtype CH3 not found ( as expected, i know why it happens). hence my question is how to use oplsaa for decane molecule?
> Regards
> Vinoth
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