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 - 04:30:02 PDT
