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()
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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Received on Thu May 05 2011 - 07:30:02 PDT
