AMBER Archive (2004)

Subject: AMBER: Disulfide bond command

From: bybaker_at_itsa.ucsf.edu
Date: Fri Jul 09 2004 - 13:16:13 CDT

('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

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