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

From: JiYuan Liu <liujiyuan.nwsuaf.edu.cn>
Date: Wed, 21 Dec 2011 10:24:32 +0800

Hi Martin,
    I have attached them,you could download.
Best Regards
JiYuan

于 2011年12月20日 21:31, Martin Peters 写道:
> 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
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>
>>
>> --
>> 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>_______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber


-- 
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




_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber


Received on Tue Dec 20 2011 - 18:30:03 PST
Custom Search