Re: [AMBER] MMPBSA: calcerror Failed with prmtop complex.prmtop

From: Vivek Shankar Bharadwaj <vbharadw.mymail.mines.edu>
Date: Thu, 31 Jul 2014 21:07:35 -0600

Hi Jason,

Some more Info.

The number of atoms in the (complex) = number of atoms in (receptor +
ligand) topology files.
However, I am running a simulation of an enzyme in an ionic liquid water
mixture. I did consider the IL to be part of the solvent and stripped it
when getting the complex prmtop.

Could this have anything to do with the NATOM mismatch?

Vivek


On Thu, Jul 31, 2014 at 8:59 PM, Vivek Shankar Bharadwaj <
vbharadw.mymail.mines.edu> wrote:

> Hi Jason,
>
> I was able to get the mdout files to output the error.
>
> It says there is 'NATOM mismatch on coord and topology files'.
>
> Vivek
>
>
> On Thu, Jul 31, 2014 at 8:51 PM, Jason Swails <jason.swails.gmail.com>
> wrote:
>
>> On Thu, Jul 31, 2014 at 9:23 PM, Vivek Shankar Bharadwaj <
>> vbharadw.mymail.mines.edu> wrote:
>>
>> > Hi there,
>> >
>> > I am trying to calculate binding energies using MMGBSA for a
>> carbohydrate
>> > molecule (built using Glycam06 FF) in an enzyme. I keep running into the
>> > error,
>> >
>> > CalcError: /home/common/packages/amber12/bin/mmpbsa_py_energy failed
>> with
>> > prmtop complex.prmtop!
>> >
>> > I looked for an error in the _MMPBSA_complex_gb.mdout.0 file but it is
>> > empty.
>> >
>> > I tried to run mmpbsa_py_energy alone using the following command and I
>> get
>> > a segmentation fault.
>> >
>> > -- mmpbsa_py_energy -i _MMPBSA_gb.mdin -p complex.prmtop -c
>> > _MMPBSA_complex.pdb -y _MMPBSA_complex.mdcrd.0
>> >
>>
>> ‚ÄčThis is strange. There may be an error in your files of some sort that
>> mmpbsa_py_energy just doesn't pick up. It's possible that sander may
>> produce a more helpful error message if, indeed, there is some sort of
>> problem.
>>
>> What happens when you set "use_sander=1" in the &general section of your
>> input file?
>>
>> --
>> Jason M. Swails
>> BioMaPS,
>> Rutgers University
>> Postdoctoral Researcher
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
>
> --
> Vivek S. Bharadwaj
> Graduate Student
> Department of Chemical and Biological Engg.
> Colorado School of Mines
> Golden Colorado
>



-- 
Vivek S. Bharadwaj
Graduate Student
Department of Chemical and Biological Engg.
Colorado School of Mines
Golden Colorado
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Received on Thu Jul 31 2014 - 20:30:03 PDT
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