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, Vivek 2008/11/7 Kukol, Andreas <[EMAIL PROTECTED]> > 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: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] > 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 > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php >
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