AMBER: problems with bonding disulfide linkages

From: Beale, John <>
Date: Mon, 19 Feb 2007 14:39:10 -0600

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


John Beale



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Received on Wed Feb 21 2007 - 06:07:33 PST
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