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 - 05:00:02 PDT
