Re: [AMBER] MTK++ and MCPB patch released

From: JiYuan Liu <>
Date: Tue, 20 Dec 2011 21:04:37 +0800

Hi Martin,
I have attached them,you could download them to have a test.I am
waitting for your reply.Thank you.
Best Regards

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 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
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> AMBER mailing list

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

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Received on Tue Dec 20 2011 - 05:30:02 PST
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