AMBER: how to simulate a ligand bound to a residue

From: Jena M <>
Date: Thu, 18 Oct 2007 14:49:55 +0100

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
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Received on Sun Oct 21 2007 - 06:07:28 PDT
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