Re: AMBER: problems with bonding disulfide linkages

From: Pankaj R. Daga <>
Date: Mon, 19 Feb 2007 16:54:24 -0600

Hey John,

I was just wondering if you had editted the protein file before using Leap. The CYS residue names, involved in disulfide bonds, need to be changed to CYX.

Hope this helps

If your ship doesn't come in, swim out to it.......Jonathan Winters
Pankaj R. Daga |
Department of Medicinal Chemistry | e-mail:
417 Faser Hall, School of Pharmacy | fax: +1-662-915-5638
University of Mississippi | phone: +1-662-915-1853
University, MS, 38677-1848 |

----- Original Message -----
From: Beale, John
Sent: Monday, February 19, 2007 2:39 PM
Subject: AMBER: problems with bonding disulfide linkages

I am trying to set up a protein that contains 7 disulfide bonds. When I set up the molecule through leap without first using the "bond" command for the disulfides, the amber parameters *.top and *.crd are saved properly. When I go back into leap and add one of the -S-S- bonds, leap gives the following warnings:
Could not find:
Bond parameters for SH-SH
Angle parameters for HS-SH-SH
Proper torsions;
No torsion terms for: HS-SH-SH-CT
A total of 217 improper torsions applied.
If I bond all 7 disulfides the number of these warnings is just multiplied. These seem like very strange bond, angle, and torsion parameters to me. For instance, there shouldn't be an SH-SH bond in the molecule, or an HS-SH-SH angle.
Can someone tell me what I need to do to work through this? I am using Amber 9 and have tried the ff03 and ff99 forcefields, getting the same warnings.
John Beale
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Received on Wed Feb 21 2007 - 06:07:35 PST
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