AMBER Archive (2007)

Subject: AMBER: problems with bonding disulfide linkages

From: Beale, John (jbeale_at_stlcop.edu)
Date: Mon Feb 19 2007 - 14:39:10 CST

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

                               SH-SH-CT

                               SH-SH-HS

 

Proper torsions;

No torsion terms for: HS-SH-SH-CT

                               HS-SH-SH-HS

                              CT-SH-SH-CT

                               CT-SH-SH-HS

 

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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