Re: [AMBER] Regarding Protein-ligand MD

From: FyD <>
Date: Tue, 28 Oct 2014 10:02:22 +0100

Dear Bikash Ranjan Sahoo,

You could use R.E.D. Server Dev./PyRED at

See tutorial:

I guess you have to generate a molecular fragment such as:

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
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