Dear Amber users, a bit related problem - is it ok to parametrize files in Amber11 with zinc containing protein using MCPB and then to run sander from Amber10 on it?
Best regards,
Andrew
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21.11.2011, 20:07, "Andrew Voronkov" <drugdesign.yandex.ru>:
Sure, thank you!
Best regards,
Andrew
18.11.2011, 21:20, "Martin Peters" <martin.b.peters.me.com>:
> šHi Andrew,
>
> šThere is no HE1 residue in the pdb file. šEdit the file and retry.
>
> šRegards,
> šMartin
>
> šOn 18 Nov 2011, at 14:57, Andrew Voronkov wrote:
>> ššDear Amber users, I am trying to parametrize Zn containing protein with CCCH coordination and get an error provided below.
>> ššI 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:
>> ššhttp://archive.ambermd.org/201108/0749.html
>>
>> ššPDB, prep and šfrcmod files are attached.
>>
>> ššCould not find bond parameter for: NA - ZN
>> ššBuilding angle parameters.
>> ššCould not find angle parameter: S2 - ZN - NA
>> ššCould not find angle parameter: CR - NA - ZN
>> ššCould not find angle parameter: H - NA - ZN
>> ššCould not find angle parameter: NA - ZN - S2
>> ššCould not find angle parameter: NA - ZN - S2
>> ššCould not find angle parameter: CC - NA - ZN
>> ššBuilding proper torsion parameters.
>> šš** No torsion terms for šS2-ZN-NA-CC
>> šš** No torsion terms for šS2-ZN-NA-H
>> šš** No torsion terms for šS2-ZN-NA-CR
>> šš** No torsion terms for šCT-S2-ZN-NA
>> šš** No torsion terms for šCR-NA-ZN-S2
>> šš** No torsion terms for šCR-NA-ZN-S2
>> šš** No torsion terms for šH-NA-ZN-S2
>> šš** No torsion terms for šH-NA-ZN-S2
>> šš** No torsion terms for šNA-ZN-S2-CT
>> šš** No torsion terms for šNA-ZN-S2-CT
>> šš** No torsion terms for šCC-NA-ZN-S2
>> šš** No torsion terms for šCC-NA-ZN-S2
>>
>> ššPS is there anyone who can answer the question? I have asked similar question couple of weeks ago, but got no answer.
>>
>> ššSincerely yours,
>> ššAndrew<ZN2.prep><ZN2.frcmod><3mhj2.pdb>_______________________________________________
>> ššAMBER mailing list
>> ššAMBER.ambermd.org
>> ššhttp://lists.ambermd.org/mailman/listinfo/amber
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Received on Thu Nov 24 2011 - 12:30:02 PST
