Hi JiYuan,
Two final files are required:
caparm.xml and calib.xml
Regards,
Martin
On 20 Dec 2011, at 13:04, JiYuan Liu wrote:
> Hi Martin,
> I have attached them,you could download them to have a test.I am waitting for your reply.Thank you.
> Best Regards
> JiYuan
>
>
>
> 于 2011年12月20日 17:08, Martin Peters 写道:
>> Hi JiYuan,
>>
>> Please send us all the files necessary to reproduce the problem:
>>
>> 3H68_OH_resNames.bcl
>> 3H68_OH_settings.bcl
>> 3H68_OH_params_fc_md.xml
>> 3H68_OH_chg2.xml
>> 3H68_OH_stdMol.xml
>> 3H68_OH_fixed_H.pdb
>>
>> Regards,
>> Martin
>>
>> On 20 Dec 2011, at 02:37, JiYuan Liu wrote:
>>
>>> Hi Ben,
>>> I have updated MTK++ and MCPB patch released,but the situation changed
>>> more worse,so I recoveried my Amber11 and ambertools11.
>>> By the way,I have attached all of files in the maillist with the title "The
>>> charge is wrong when the ligand together with the large model in MCPB",you
>>> could help me to test it,I want to know 3 things which I can not solve.
>>> 1. a command findMetalCenters in 3H68_OH_resNames.bcl,when I run this BCL
>>> script,I can' t get the complete bond informations between atom to atom in
>>> 3H68_OH.leaprc;
>>> 2. in 3H68_OH_resNames.bcl,I checked one of the results with
>>> 3H68_OH_mcpb.pdb,it can't Write pdb with new residue names,the residues
>>> which are coordinated with ZN ions could not be change their original name
>>> into the new name as HD1 AS1 et al.
>>> You can refer to these from my attachments.
>>> 3. When I runed the min.in with the parmtop that be generated by MCPB, the
>>> two ZN ions is stable after the minimization, but the ligand is deformed
>>> very serious.
>>> I was very warried about these errors,please help me,thank you.
>>> Best Regards
>>> JiYuan
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>
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>>
>
>
> --
> Jiyuan Liu
> Key Laboratory of Plant Protection Resources and Pest Management,National Ministry of Education
> Northwest A&F University
> Yangling, Shaanxi
> China 712100
> Phone: 86-29-87092190
>
> <3H68_OH_resNames.bcl><3H68_OH_settings.bcl><3H68_OH_params_fc_md.xml><3H68_OH_chg2.xml><3H68_OH_stdMol.xml><3H68_OH_fixed_H.pdb>_______________________________________________
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Received on Tue Dec 20 2011 - 06:00:04 PST
