Re: AMBER: how to simulate a ligand bound to a residue

From: FyD <>
Date: Thu, 18 Oct 2007 23:02:13 +0200

Quoting Jena M <>:

> 1) I want to derive charges for the ligand-cysteine using resp
> procedure. Could someone please tell me how to fix the partial
> charges for the Calpha-linking atoms (CA, C, N,O,H,HA)of cysteine
> with the values of a cysteine residue in amber force field? Should I
> fix these charges in the Gaussian input file or in antechamber? How?

You could look at the tutorial available .

You could also look at some Cysteine derivatives already available in
see the following projects:
F-70 Central fragment of S-methyl-L-cysteine
F-69 Central fragment of S-methyl-L-cysteine
F-68 Central fragment of S-sulfonate-L-cysteine
F-67 Central fragment of S-sulfonate-L-cysteine
F-66 Central fragment of sulfonate-L-cysteine
F-65 Central fragment of sulfonate-L-cysteine

To fix a charge to a particular value you need to use (an)
intra-molecular charge constraint(s) during the RESP fit (see again
the tutorial).

> 2) I have parameters for the bond, angle and dihedrals involving the
> C(ligand)-S(cys) connection. I defined a new atom type for S (SV).
> For the ligand I used gaff parameters and hence I mixed gaff and
> amber atoms types while setting the parameters for the
> C(ligand)-S(cys) connection in the frcmod file (for example
> c3-c3-SV-CT). Is there any problem with this?

If you do not want to derive your own FF parameters your strategy
seems correct. However, it is always interesting to run some QM
geometry optimization for your new molecule to see at least if the
minima you are going to get are in agreement with the structures
observed during MD simulations.

regards, Francois

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Received on Sun Oct 21 2007 - 06:07:34 PDT
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