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

From: Thomas Steinbrecher <>
Date: Thu, 18 Oct 2007 11:29:25 -0700 (PDT)

Hi Jeninha,

1) You could put ACE and NME endgroups on your ligand-cysteine
compound and derive resp charges for that. They should turn out to be very
similar to the ones that an actual cysteine residue has. I wouldnt fix
any charges, your ligand will slightly change the former cysteines
electrostatics anyway.

2) Combining gaff and amber types in a system is ok and they were designed
for that. Combining both types in one residue is an unusual idea,
because then you have to come up with all parameters that cross the
boundary. If you have those however, it should not be to tricky to do.

Im no expert on this, so other people might have profounder advice to



Dr. Thomas Steinbrecher
The Scripps Research Institute
10550 N. Torrey Pines Rd.
San Diego CA 92037, USA

On Thu, 18 Oct 2007, Jena M wrote:

> Dear amber users,
> I have some questions about how to create input files for a ligand bound to a cysteine of a peptide:
> 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?
> 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?
> Thanks in advance
> Jeninha
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Received on Sun Oct 21 2007 - 06:07:32 PDT
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