Dear Carlos,
Thanks for your kind reply.
Best,
Sudip
On Mon, Oct 31, 2016 at 5:23 PM, Carlos Simmerling <
carlos.simmerling.gmail.com> wrote:
> This is the Amber support list, but you're using the GROMOS force field and
> GROMACS software. There could be many reasons for what you're seeing, but
> none of them are related to Amber so it's difficult to offer any advice
> other than to check with the GROMOS or GROMACS support.
>
> On Mon, Oct 31, 2016 at 7:07 AM, Sudip Das <das.sudip37.gmail.com> wrote:
>
> > Dear All,
> >
> > I am performing simulation of a protein containing cyclic peptide ring
> (not
> > an regular amino acid) using GROMOS54a7 force field with GROMACS 5.0.5
> > package. After equilibration and NVT production run, the final structure
> > having a C-CHn-CHn-C dihedral angle has a value of -18.5 degree, whereas
> > after optimizing the final structure quantum chemically in Gaussian09
> > software, the same dihedral angle gives the value equal to +18.1 degree.
> >
> > Can anyone please suggest any solution? Should I need to change the
> > dihedral angle parameter in the force field? Or this is just a problem of
> > sign convention between the above to computing softwares?
> >
> > Thanks in advanced.
> >
> > Regards,
> > Sudip
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Received on Mon Oct 31 2016 - 05:30:04 PDT
