Also, it looks that you have N1 (ND1) instead of NA (NE2) that bound to Zn, according to your prep and frcmod files, but you were asking leap to connect Zn to NA (NE2) which cause leap cannot find the proper parameters. Correct the corresponding 'bond' statement in your leap input and make another try.
Yue
On Nov 18, 2011, at 9:57 AM, 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 - 12:30:02 PST
