Hi Andrew,
There is no HE1 residue in the pdb file. Edit the file and retry.
Regards,
Martin
On 18 Nov 2011, at 14:57, Andrew Voronkov wrote:
> 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<ZN2.prep><ZN2.frcmod><3mhj2.pdb>_______________________________________________
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Received on Fri Nov 18 2011 - 09:30:04 PST
