Dear Bikash Ranjan Sahoo,
You could use R.E.D. Server Dev./PyRED at
http://q4md-forcefieldtools.org/REDServer-Development/
See tutorial:
http://q4md-forcefieldtools.org/Tutorial/Tutorial-4.php
I guess you have to generate a molecular fragment such as:
http://q4md-forcefieldtools.org/Tutorial/Tutorial-4.php#16
regards, Francois
> I am facing some problems in simulating a P-L complex where the
> ligand is covalently bonded to the protein with two adjacent residues. The
> ligand is a unnatural amino acid. In such scenario, I came across the
> Paramfit tutorial where it is possible to generate a FF from the inputs. Is
> it possible to generate a force field for such a system that will hold all
> connecting information (covalent bonded information) between the ligand
> and protein. If it is possible, can somebody suggest how long it will take
> to generate force field parameters for ~200 AA long system.
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Received on Tue Oct 28 2014 - 02:30:02 PDT
