Re: [AMBER] Regarding Protein-ligand MD

From: Robin Betz <>
Date: Mon, 27 Oct 2014 20:02:48 -0700

Hi Bikash,

Creating parameters not present in conventional force fields is what
Paramfit was designed for.

However, part of the process involves doing QM calculations on many
conformations of your system, and 200 AA is much too large for this. I
would suggest taking a subset of your structure, for example just the
ligand and whatever amino acids it is bound to, and fitting parameters to
that smaller system.

Robin Betz

On Mon, Oct 27, 2014 at 7:58 PM, Bikash Ranjan Sahoo <> wrote:

> 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
> Bikash
> _______________________________________________
> AMBER mailing list
AMBER mailing list
Received on Mon Oct 27 2014 - 20:30:03 PDT
Custom Search