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
>>>>>>> _______________________________________________
>>>>>>> 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
>
> _______________________________________________
> 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
Received on Thu Dec 22 2011 - 05:30:02 PST
