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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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Received on Fri Jul 09 2004 - 19:53:00 PDT
