AMBER Archive (2009)

Subject: Re: [AMBER] enquiry regarding parameter file to be used

From: bharat lakhani (lakhbharat_at_gmail.com)
Date: Thu Nov 19 2009 - 23:35:14 CST

ok for protein i am using .ff99 and for ligand molecule. first i run the
antechamber then i have created prepin and frcmod file. for generating
parameters i am using leaprc.gaff, loadamberprep, loadamberparam commands

On Mon, Nov 16, 2009 at 5:10 PM, Carlos Simmerling <
carlos.simmerling_at_gmail.com> wrote:

> we need more information.
>
>
> On Sat, Nov 14, 2009 at 12:52 AM, bharat lakhani <lakhbharat_at_gmail.com
> >wrote:
>
> > I am using .ff99 force field parameter.
> >
> > On 11/13/09, Carlos Simmerling <carlos.simmerling_at_gmail.com> wrote:
> > >
> > > the energy keeps going down- I suspect a problem with your force field
> > > parameters. perhaps you could tell people how you generated the
> > parameters.
> > >
> > > On Fri, Nov 13, 2009 at 8:35 AM, bharat lakhani <lakhbharat_at_gmail.com
> > > >wrote:
> > >
> > > > please find the attachment
> > > > parameter thats been used for this system
> > > > ncyc=500
> > > > igb=5
> > > > cut=999
> > > > still minimisation not working.
> > > > Revert please.
> > > >
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