You can try adding "use_sander=1" to the &general section. I *think* that
your prmtop and coordinate files are inconsistent in some way (that is,
your complex prmtop is not exactly the same as your solvated prmtop minus
the strip_mask contents, and your receptor + ligand prmtops are not exactly
the same as your complex prmtop). A mismatch of coordinates can cause
weird behavior. The point of using "use_sander=1" is to *hopefully* get a
more helpful error message.
Another thing worth trying is adding netcdf=1 to the &general section,
since NetCDF files contain more information than ASCII trajectories.
HTH,
Jason
On Mon, Apr 4, 2016 at 8:17 AM, sunita gupta <sunita.bio.gmail.com> wrote:
> Thanks for the suggestion.
> I tried with single trajectory calculation and use 3 different systems for
> calculation. But every time I am getting the same error, and 3 different
> systems can not have memory issue.
> I think Lig.prm which is actually a SERINE molecule is having problem, as
> everytime it is stucking while producing _MMPBSA_ligand_gb.mdout.0. I also
> visualised the lig.prm and lig.crd in VMD...but it looked fine.
>
> Has anyone ever faced such problem, when dealing with protein-peptide
> system...?
>
>
>
>
> On Fri, Apr 1, 2016 at 5:52 PM, Bill Miller III <brmilleriii.gmail.com>
> wrote:
>
> > Hi,
> >
> > Sounds like you may be running out of RAM for his calculation on your
> > current computer. PB calculations are known to be relatively memory
> > intensive. How large is your system? Potentially try using just the GB
> > protocol which uses less memory than PB.
> >
> > Hope that helps.
> >
> > -Bill
> >
> > > On Apr 1, 2016, at 1:22 AM, sunita gupta <sunita.bio.gmail.com> wrote:
> > >
> > > Hello everyone,
> > >
> > > I am trying to calculate the binding energy using MMPBSA.py (Amber12).
> I
> > > have a trimer structure with serine bound at the active site between
> two
> > > chains. I made the complex.prm and complex.crd file using ff99SB
> > forcefield
> > > (as the ligand is also a peptide) and did simulation for 5 ns.
> > >
> > > Later with tleap again I made complex.prm. receptor.prm and lig.prm,
> with
> > > striped off WAT and NA and sublected to MMPBSA calculation.
> > >
> > > I am getting the error "**** glibc detected
> > > ***.....amber12/bin/mmpbsa_py_energy: malloc(): memory corruption:
> > > 0x00000000027075e0 ****"
> > > *CalcError: ....amber12/bin/mmpbsa_py_energy failed with prmtop
> > > lig_tleap.prm!*
> > >
> > >
> > >
> > > This is the mmpbsa.in file I am using
> > > Input file for running PB and GB in serial
> > > &general
> > > startframe=249, endframe=250, keep_files=2, strip_mask=":WAT:NA"
> > > /
> > > &pb
> > > istrng=0.100, exdi=80.0, indi=1.0,
> > > /
> > >
> > > Thanks in advance
> > > --
> > > --
> > > SUNITA GUPTA
> > > PhD Scholar
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> >
> > _______________________________________________
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> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> --
> SUNITA GUPTA
> PhD Scholar
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
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Received on Mon Apr 04 2016 - 07:00:04 PDT
