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