Sure, thank you!
Best regards,
Andrew
18.11.2011, 21:20, "Martin Peters" <martin.b.peters.me.com>:
> Hi Andrew,
>
> There is no HE1 residue in the pdb file. šEdit the file and retry.
>
> Regards,
> Martin
>
> On 18 Nov 2011, at 14:57, Andrew Voronkov wrote:
>
>> šDear Amber users, I am trying to parametrize Zn containing protein with CCCH coordination and get an error provided below.
>> šI 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:
>> šhttp://archive.ambermd.org/201108/0749.html
>>
>> šPDB, prep and šfrcmod files are attached.
>>
>> šCould not find bond parameter for: NA - ZN
>> šBuilding angle parameters.
>> šCould not find angle parameter: S2 - ZN - NA
>> šCould not find angle parameter: CR - NA - ZN
>> šCould not find angle parameter: H - NA - ZN
>> šCould not find angle parameter: NA - ZN - S2
>> šCould not find angle parameter: NA - ZN - S2
>> šCould not find angle parameter: CC - NA - ZN
>> šBuilding proper torsion parameters.
>> š** No torsion terms for šS2-ZN-NA-CC
>> š** No torsion terms for šS2-ZN-NA-H
>> š** No torsion terms for šS2-ZN-NA-CR
>> š** No torsion terms for šCT-S2-ZN-NA
>> š** No torsion terms for šCR-NA-ZN-S2
>> š** No torsion terms for šCR-NA-ZN-S2
>> š** No torsion terms for šH-NA-ZN-S2
>> š** No torsion terms for šH-NA-ZN-S2
>> š** No torsion terms for šNA-ZN-S2-CT
>> š** No torsion terms for šNA-ZN-S2-CT
>> š** No torsion terms for šCC-NA-ZN-S2
>> š** No torsion terms for šCC-NA-ZN-S2
>>
>> šPS is there anyone who can answer the question? I have asked similar question couple of weeks ago, but got no answer.
>>
>> šSincerely yours,
>> šAndrew<ZN2.prep><ZN2.frcmod><3mhj2.pdb>_______________________________________________
>> šAMBER mailing list
>> šAMBER.ambermd.org
>> šhttp://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Mon Nov 21 2011 - 08:30:04 PST
