Re: [AMBER] metal ion parameterisation problem

From: Kshatresh Dutta Dubey <kshatresh.gmail.com>
Date: Mon, 23 Jun 2014 18:02:06 +0300

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,
> >
> > 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
> > --
> > 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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>
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Received on Mon Jun 23 2014 - 08:30:02 PDT
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