[AMBER] Regarding Protein-ligand MD

From: Bikash Ranjan Sahoo <bikash.bioinformatics.gmail.com>
Date: Tue, 28 Oct 2014 11:58:33 +0900

Dear All,
            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.

Best Regards
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Received on Mon Oct 27 2014 - 20:00:02 PDT
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