hi
thanx so muxh for the help but i would like to explain what i intend
to do. i have to carry out MD simulations of a phe-phe dipeptide and
phe-delphe dipeptide. i had all the parameters for del phe peptide and
so i have modelled both phe-phe and phe-delphe using SYBYL. now when i
load the dipeptide in xleap, there i see a difference in the atom
names since both the propgrams must be following some diffrenet atom
name conventions.
when i load the phe-phe dipeptide in xleap, it tells me some wrong
torsional angles etc. now in order to correct them in frcmod file i
need to know what atom do these correspond to(which i am not able to
do due to different atom name convention)
please tell me where i am goin wrong or what should i do. i will be thankful.
for your reference i am attaching my phe-phe mol2 file.
thanx
On 2/26/07, bertrand russell <betrussell23.gmail.com> wrote:
> 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.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.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
> > >
> > -----------------------------------------------------------------------
> > The AMBER Mail Reflector
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> >
>
>
>
> --
> Live Life; Don't pass it
> Bertrand.P.S.Russell
> +91-9894398441
>
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Received on Wed Feb 28 2007 - 06:07:32 PST
