Re: [AMBER] metal ion parameterisation problem

From: Pengfei Li <ambermailpengfei.gmail.com>
Date: Wed, 25 Jun 2014 16:25:54 -0400

Hi Kshatresh,

Sorry for the late reply. Actually it doesn't show the information about
which water is wrong when adding the hydrogens in the output log file so
I am not sure about it.
 
I would suggest that if you meet this problem later you can use other tools to
adding the hydrogens first and perform the following calculation based on
that structure by using MCPB.

Hope it helps.

Best,
Pengfei

On Jun 23, 2014, at 3:52 PM, Kshatresh Dutta Dubey <kshatresh.gmail.com> wrote:

> Dear Li,
>
> Thank you very much for your cooperation. I will be thankful if you
> tell me the process to point out that specific water, so that I would not
> disturb you for the next time.
>
> Thank you again
>
> Regards
> Kdd
>
>
> On Mon, Jun 23, 2014 at 9:53 PM, Pengfei Li <ambermailpengfei.gmail.com>
> wrote:
>
>> Hi Kshatresh,
>>
>> I checked the file and it seems the error comes from the adding hydrogens
>> for one of the water molecules.
>>
>> I added the hydrogens for the HOH residues by using tleap. The attachment
>> is the pdb after doing that.
>>
>> You can use this pdb and continue to add the hydrogens to the amino acid
>> and MOH residues by using MCPB.
>>
>> Best,
>> Pengfei
>>
>>
>>
>> On Jun 23, 2014, at 11:02 AM, Kshatresh Dutta Dubey <kshatresh.gmail.com>
>> wrote:
>>
>>> Hi Roberts,
>>>
>>> Thanks for your cooperation. I have attached the all bcl scripts and
>>> other files. Since error was in initial staged so I used following two
>>> commands:
>>>
>>> 1- sh genMetalFF.sh -n protein
>>>
>>> 2- MCPB -i protein_addHs.bcl -l protein_addHs.bcl.log
>>>
>>> for add hydrogen utility that gave following error
>>>
>>> 1 Error in watProtonate ... exiting
>>> terminate called after throwing an instance of 'MTKpp::MTKException'
>>> Aborted (core dumped)
>>>
>>>
>>> Regards
>>> Kshatresh
>>>
>>>
>>> On Mon, Jun 23, 2014 at 5:10 PM, Ken Merz <kmerz1.gmail.com> wrote:
>>>
>>>> Hi Ben,
>>>>
>>>> Pengfei has gained expertise with MTK++ as well and can help out as
>>>> needed. Hope all is well!
>>>>
>>>> Kennie
>>>>
>>>> On Jun 22, 2014, at 5:57 PM, Ben Roberts <ben.roberts.geek.nz> wrote:
>>>>
>>>>> Hi Kshatresh,
>>>>>
>>>>> Iíve seen problems of this kind in MTK++ and MCPB before, and may be
>>>> able to help you (though it may take a while as I will have to do so in
>> my
>>>> spare time, and I appreciate your patience). Could you please send a
>>>> tarball containing a list of the commands youíve run, your BCL scripts,
>> and
>>>> the original and generated PDB files?
>>>>>
>>>>> Regards,
>>>>> Ben
>>>>> --
>>>>> For greater security, I support S/MIME encryption.
>>>>>
>>>>> On 21/06/2014, at 9:29 am, Kshatresh Dutta Dubey <kshatresh.gmail.com>
>>>> wrote:
>>>>>
>>>>>> Dear Users,
>>>>>>
>>>>>> I am using MPCB for metal ion parameterisation of an enzyme
>>>> containing
>>>>>> iron coordinated with three histidine. I followed the tutorial for
>> MCPB.
>>>>>> During *MCPB -i FEHID_addHs.bcl -l FEHID_addHs.bcl.log *run, MCPB
>>>>>> terminates with error:
>>>>>> '1 Error in watProtonate ... exiting terminate called after throwing
>> an
>>>>>> instance of 'MTKpp::MTKException'
>>>>>>
>>>>>> while it runs fine with example pdb provided in tutorial. How can I
>>>> figure
>>>>>> out which water is causing problem and how to solve it? some last
>>>> lines
>>>>>> of output for log file is :
>>>>>> ### ### ### ###
>>>>>>
>>>>>> ### ### ### ###
>>>>>> ### MTK++ Info ###
>>>>>> ### Function: watProtonate::run ###
>>>>>> ### Message: sorted water energies
>>>>>> ### ### ### ###
>>>>>>
>>>>>> I will be thankful for your suggestions.
>>>>>>
>>>>>> Regards
>>>>>> Kshatresh
>>>>>> _______________________________________________
>>>>>> AMBER mailing list
>>>>>> AMBER.ambermd.org
>>>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>>>
>>>>>
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>
>
> --
> With best regards
> ************************************************************************************************
> Dr. Kshatresh Dutta Dubey
> Post Doctoral Researcher,
> c/o Prof Sason Shaik,
> Hebrew University of Jerusalem, Israel
> Jerusalem, Israel
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber


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Received on Wed Jun 25 2014 - 13:30:02 PDT
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