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
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Received on Fri Apr 01 2016 - 05:30:03 PDT
