On Thu, May 5, 2011 at 3:59 PM, <poll.chemie.uni-hamburg.de> wrote:
> Hi everybody,
>
> I just tried to calculate entropy terms using MMPBSA.py and nmode in
> Amber11.During the calculation I get the following error several
> times:
>
> mmpbsa_py_nabnmode: sff2.c:1266: ephi2: Assertion `bk > 0.01' failed.
> sh: line 1: 23006 Aborted
> /opt/amber11/bin/mmpbsa_py_nabnmode _MMPBSA_ligand_nm.pdb.46
> drg.prmtop 10000 0.001 "ntpr=10000, diel=C, kappa=0.103951911959,
> cut=1000, gb=1, dielc=4.0, temp0=298.15" >> _MMPBSA_ligand_nm.out.5
> FATAL: allocation failure in vector()
>
You are running out of memory.
This is common when you use big systems on computers with limited memory,
keep in mind that you need even more energy (twice the amount for 2
processors, 3 times the amount for 3 processors, etc.).
HTH,
Jason
>
> The calculation is completed but when I check the output files it
> tells me that the snapshots which are used for normal mode weren't
> minimized but when I check the
> _MMPBSA_ligand(receptor/complex)_nm.out
> the structures were minimized.
>
> This is the inputfile I use.
>
> Input file for running PB and GB
> &general
> endframe=50, verbose=1,
> /
> &gb
> igb=2, saltcon=0.100
> /
> &pb
> istrng=0.100,
> /
> &nmode
> nmstartframe=1, nmendframe=50,
> nminterval=5, nmode_igb=1, nmode_istrng=0.1,
> /
>
> I also use the -use-mdins flag with arcres=0.125 and gbsa=1. Hopefully
> some of you might have experience with this errors.
>
> Thanks in advance
>
> Bernhard
>
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>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Thu May 05 2011 - 07:30:03 PDT
