Dear JiYuan,
Please find attached an updated 3H68_OH_mcpb.pdb file with the metal center correctly found.
In $AMBERHOME/AmberTools/src/mtkpp/src/molecule/collection.cpp
changing the lines (around line 230):
metalDonorDists["Zn:SER"] = 1.14;
and
metalDonorDists["Zn:S"] = 1.14;
to
metalDonorDists["Zn:SER"] = 2.14;
and
metalDonorDists["Zn:S"] = 2.14;
fixes the problem. You can do the same and recompile.
This may appear strange but when a ligand oxygen is bound to a metal I use the Serine-metal distance as a reference.
The 2.14A number was problematic in other systems. I will implement a system to allow these parameters to be changed from a file.
HTH,
Martin
On 21 Dec 2011, at 02:24, JiYuan Liu wrote:
> 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
>
> <caparm.xml><calib.xml>_______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
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Received on Thu Dec 22 2011 - 03:00:02 PST
