AMBER: Disulfide bond command

From: <>
Date: Fri, 09 Jul 2004 11:16:13 PDT
('binary' encoding is not supported, stored as-is) Hello, Amber:

My question is about how to add bond information about disulfide bond. I
notice that some one post the same question before, but I could not found
the answer for it from Amber mail-relector. So I post the question again,
and hope to get some help.

I tried to load my .pdb file with tleap. The file contains one disufide
bond. I use bond command as described in manual:
bond test.100.SG test.261.SG

And 'saveAmberParm' but get the following messages:

> bond test.100.SG test.261.SG
> saveAmberParm test test.prmtop test.inpcrd
Checking Unit.
WARNING: The unperturbed charge of the unit: -2.000000 is not zero.

 -- ignoring the warning.

Building topology.
Building atom parameters.
Building bond parameters.
Could not find bond parameter for: SH - SH
Building angle parameters.
Could not find angle parameter: HS - SH - SH
Could not find angle parameter: SH - SH - CT
Could not find angle parameter: SH - SH - HS
Could not find angle parameter: CT - SH - SH
Building proper torsion parameters.
 ** No torsion terms for HS-SH-SH-CT
 ** No torsion terms for HS-SH-SH-HS
 ** No torsion terms for CT-SH-SH-CT
 ** No torsion terms for CT-SH-SH-HS
Building improper torsion parameters.
 total 634 improper torsions applied
Building H-Bond parameters.
Parameter file was not saved.

Can anyone please let me know how to fix the problem?

Thank you

Bo Yang

The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to
Received on Fri Jul 09 2004 - 19:53:00 PDT
Custom Search