Re: [AMBER] metal ion parameterisation problem

From: Pengfei Li <ambermailpengfei.gmail.com>
Date: Mon, 23 Jun 2014 14:53:46 -0400

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
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>>>
>>>
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Received on Mon Jun 23 2014 - 12:00:02 PDT
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