Re: [AMBER] metal ion parameterisation problem

From: Ben Roberts <ben.roberts.geek.nz>
Date: Mon, 23 Jun 2014 09:57:11 +1200

Hi Kshatresh,

I’ve 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 you’ve run, your BCL scripts, and the original and generated PDB files?

Regards,
Ben

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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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Received on Sun Jun 22 2014 - 15:00:01 PDT