Dear Amber users, I am trying to parametrize Zn containing protein with CCCH coordination and get an error provided below.
I ve checked the names for residues - they are ZN for Zn atom and CY2 for cysteins which it should bind. The parameters were generated by MCPB using script provided here:
http://archive.ambermd.org/201108/0749.html
PDB, prep and frcmod files are attached.
Could not find bond parameter for: NA - ZN
Building angle parameters.
Could not find angle parameter: S2 - ZN - NA
Could not find angle parameter: CR - NA - ZN
Could not find angle parameter: H - NA - ZN
Could not find angle parameter: NA - ZN - S2
Could not find angle parameter: NA - ZN - S2
Could not find angle parameter: CC - NA - ZN
Building proper torsion parameters.
** No torsion terms for S2-ZN-NA-CC
** No torsion terms for S2-ZN-NA-H
** No torsion terms for S2-ZN-NA-CR
** No torsion terms for CT-S2-ZN-NA
** No torsion terms for CR-NA-ZN-S2
** No torsion terms for CR-NA-ZN-S2
** No torsion terms for H-NA-ZN-S2
** No torsion terms for H-NA-ZN-S2
** No torsion terms for NA-ZN-S2-CT
** No torsion terms for NA-ZN-S2-CT
** No torsion terms for CC-NA-ZN-S2
** No torsion terms for CC-NA-ZN-S2
PS is there anyone who can answer the question? I have asked similar question couple of weeks ago, but got no answer.
Sincerely yours,
Andrew
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- application/octet-stream attachment: ZN2.prep
- application/octet-stream attachment: 3mhj2.pdb
Received on Fri Nov 18 2011 - 07:00:03 PST
