I am running MMPBSA.py on an extracted trajectory that contains 8088
configurations.
The input is listed below:
&general
verbose=2, strip_mdcrd=1, strip_mask=":WAT",
entropy=0, startframe=80, endframe=8088, interval=80
/
&decomp
idecomp=2, dec_verbose=3,
/
&gb
igb=5, saltcon=0.150
/
&pb
istrng=0.150
/
&nmode
nmstartframe=10, nmendframe=100, nminterval=10,
maxcyc=50000, drms=0.0001, nmode_igb=1, nmode_istrng=0.1,
/
The submission script is here:
#!/bin/bash
#PBS -N MM_lig
#PBS -j oe -V
#PBS -q serial_std
#PBS -l select=1:ncpus=1
#PBS -m e
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/share/apps/intel/lib/intel64
cd $PBS_O_WORKDIR
MMPBSA=/share/apps/amber11/bin/MMPBSA.py
PYTHON="/share/apps/python27/bin/python2.7"
SUB="$PYTHON $MMPBSA -O -i decomp_lig.in -o decomp_lig.dat -sp
../cbp_ro3_200_py
.top -cp ../cbp_ro3_nw_py.top -rp ../cbp_3dwy_py.top -lp ../ro3_py.top -y
../cbp
_ro3_cob.c0 -do cbp_ro3_decnw.dat"
echo $SUB
$SUB
However, after 16 frames I encounter this error message:
minimizing coord set # 16
PB Bomb in assignlvlset(): no atmsas 125 74 35
123 76 37 -2
123 76 37 -2
123 76 37 2
123 76 37 -2
123 76 37 -2
123 76 37 2
123 76 37 -2
PB Bomb in assignlvlset(): illegal insas flag 125 74 35 -4
I am not sure where this error comes from or what are the indices listed. I
tentatively traced it to the pb_ionmap subroutine but I do not know how to
fix it.
I might add that changing the startframe or the interval in the input
produces a PB Bomb in a different location with different indices.
I would be grateful for any help.
Rami
Roman Osman
Department of Structural and Chemical Biology
(212) 659-8627
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Received on Tue Jul 26 2011 - 15:30:03 PDT
