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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> http://lists.ambermd.org/mailman/listinfo/amber
>
--
--
SUNITA GUPTA
PhD Scholar
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Received on Mon Apr 04 2016 - 05:30:03 PDT
