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,
> >>>
> >>> 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
> >>>> _______________________________________________
> >>>> 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
> >>
> >>
> >> _______________________________________________
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> >>
> > <MCPB.tar.bz2>_______________________________________________
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> > http://lists.ambermd.org/mailman/listinfo/amber
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>
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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
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Received on Mon Jun 23 2014 - 13:00:04 PDT
