Hi Martin,
Thank you very much.I have looked for the attachments,it looks fine that
can get the metal center correctly.Because I added the intel compilers
and cuda technology to accelerate the calculation of Amber,it took me so
long time to
recompile it for the bugfix25 in the recent time.I would make sure that
if I change the lines of collection.cpp,could it fix those previous
problems below:
1. 3H68_OH_resNames.bcl,it can write pdb with new residue names like
HD1,HD2,CA1 et al. now?
2. 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.Does the ligand become stable now?
By the way if I change the lines of collection.cpp and recompile
ambertools,could I recalculate the Side Chain Model
Optimization/Frequency Calculation and Large Model Charge Calculation?
Best Regards
JiYuan
? 2011?12?22? 18:38, Martin Peters ??:
> 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
>>
>> ? 2011?12?20? 21:31, Martin Peters ??:
>>> 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
>>>>
>>>>
>>>>
>>>> ? 2011?12?20? 17:08, Martin Peters ??:
>>>>> 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
>
>
> _______________________________________________
> 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
_______________________________________________
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Received on Thu Dec 22 2011 - 05:00:02 PST
