[gmx-users] Reg: Prodrg topology

[vinothkumar mohanakrishnan]

Thank you mark for your suggestion. can i use x2top to generate topology for
oplsaa force field by using (all atom) .gro file from PRODRG?.Is it worth
using it.

Regards
Vinoth

On Tue, Oct 5, 2010 at 11:30 AM, Mark Abraham <mark.abraham at anu.edu.au>wrote:

> 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
>
> Mark
>
> ----- 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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