AMBER Archive (2007)

Subject: Re: AMBER: phe-phe molecule

From: bertrand russell (betrussell23_at_gmail.com)
Date: Mon Feb 26 2007 - 02:03:27 CST

Hai,

Fine. One in formation would be useful to solve your query I think. Whether
you are using ff99 forcefield or ff03? If you are using ff03 then its better
to follow the ff03 lib instead of ff99. If your phe-phe is a dipeptide, then
I couldn't guess why do you want to generate .frcmod and prepin file?

On 2/26/07, deepti nayar <deepti.icgeb_at_gmail.com> wrote:
>
> thanx so much for the help but i am still a bit confused. do i have to
> use the convention followed in uni_aminont03.in or the one which is
> given in ff09 force field. please help me so that i can proceed with
> my work.
>
> deepti
>
> On 2/26/07, bertrand russell <betrussell23_at_gmail.com> wrote:
> > Hai Deepti,
> >
> > THe atom types which amber using will be in your library files directory
> > under,
> >
> > ~/amber9/dat/leap/lib under this directory you can find libraries for
> the
> > forcefield ahich you are calling while doing leap. You can refer these
> and
> > accordingly make chnges in your mol file. Hope this would work.
> >
> > With regards,
> > --
> > Live Life; Don't pass it
> > Bertrand.P.S.Russell
> > +91-9894398441
> >
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-- 
Live Life; Don't pass it
Bertrand.P.S.Russell
+91-9894398441

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