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

From: JiYuan Liu <liujiyuan.nwsuaf.edu.cn>
Date: Thu, 22 Dec 2011 22:06:19 +0800

Hi Martin,

I am sorry I could not clear express my mean about the parmtop of 3H68
in the previous emails,You may misunderstand my meaning.I would tell you
this situation follow:

Although MCPB can't get the correct metal center before change the lines
of collection.cpp,I modified the bond information in 3H68_OH.leaprc and
the residue name in 3H68_OH_mcpb.pdb by my hand,I ensured the
correctness of them before I used tleap to generate the parmtop of
3H68.I think these two files make no difference as that you sent to me.

Would you like to help me to do a test:you could use these files to
generate the parmtop and inpcrd of 3H68_OH_mcpb.pdb,and you can use the
min.in that in this attachment to run a short minimization,then you can
see the structure of the small molecule change so worsely,this is my
actual problem.

Please tell me how to only recompile mtkpp.Could you tell me why I need
to recalculate the Side Chain Model Optimization/Frequency Calculation
and Large Model Charge Calculation after I changed the lines of
collection.cpp follow your instruction.

Best Regard

JiYuan


于 2011年12月22日 21:08, Martin Peters 写道:
> Hi JiYuan,
>
> On 22 Dec 2011, at 12:41, JiYuan Liu wrote:
>
>> 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:
> All you need to do is recompile mtkpp not the whole package. Should take seconds.
>
>> 1. 3H68_OH_resNames.bcl,it can write pdb with new residue names like
>> HD1,HD2,CA1 et al. now?
> Yes, I sent you the result.
>
>> 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?
> For now don't use the prmtop file from MCPB. Create a prmtop from leap using the leaprc file i sent you.
>
>> 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?
> I don't see why not.
>
> Regards,
> Martin
>
>> 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
>>>>>>>> _______________________________________________
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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>_______________________________________________
>>>>>> 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>_______________________________________________
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>>>
>>> _______________________________________________
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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
>>
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>> 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



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Received on Thu Dec 22 2011 - 06:30:02 PST
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