[gmx-users] Running MDS over docked poses

vivek sharma viveksharma.iitb at gmail.com
Fri Nov 7 13:13:53 CET 2008

Hi Andreas,
 Thanks for your response.
But I am not finding option for AMBER forcefield in gromacs (during pdb2gmx
step). which of the 9 force-field I should use for the same.

With Thanks,

2008/11/7 Kukol, Andreas <a.kukol at herts.ac.uk>

> Hi,
> Autodock4 uses the AMBER forcefield, so that would be a good starting point
> for gromacs as well.
> In order to set the temperature for a particular group
> 1) you generate an index file containing all the atoms in your GROUP
> 2) in your mdp-file specify GROUP as a separate temperature coupling group
> and specify the temperature you want
> 3) use grompp with -n yourindexfile.ndx
> Note sure, if this is makes physically sense though.
> Andreas
> >>>>>>>>>>>>>>>>>
> From: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org]
> On Behalf Of vivek sharma
> Sent: 07 November 2008 09:00
> To: Discussion list for GROMACS users
> Subject: [gmx-users] Running MDS over docked poses
>  Hi There,
> I am trying to run MDS over some docked result generated by Autodock4, but
> I am not sure of the forcefield I should use.
> If anybody have tried doing it before, please guide me for the same. For
> generating topology of ligand, I am using PRODRG server, which has limited
> option for forcefield.
> Also, how can I give the parameters for varying temperature of a particular
> group during the MDS, like how canI define the steps I want to vary it ?
> waiting for some suggestion.
> With Thanks,
> Vivek
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