AMBER Archive (2009)

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

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Fri Nov 20 2009 - 05:20:05 CST

then you are not just using ff99 parameters. it's hard to help if we don't
know what's going on. i suggest trying the protein only and see if the
problem goes away.
for proteins it is well known that ff99 has serious problems- there is
discussino about it on this list quite often. it's very important to know
the state of the art iin such a rapidly changing field- especially if you
want to publish your work. while old simulations with ff99 may have been
useful, these days I would not view such work as being reasonable and
reviewers of manuscripts are likely to reject your submissions because of
this. you should use ff99SB in my opinion- but definitely not ff99.

On Fri, Nov 20, 2009 at 12:35 AM, bharat lakhani <lakhbharat_at_gmail.com>wrote:

> 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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