[gmx-users] Running MDS over docked poses

[Justin A. Lemkul]

vivek sharma wrote:
> 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.
>

You have to download and install the ffamber ports:

http://chemistry.csulb.edu/ffamber/

-Justin


> With Thanks,
> Vivek
> 
> 2008/11/7 Kukol, Andreas <a.kukol at herts.ac.uk <mailto: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>
>     [mailto: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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-- 
========================================

Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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