Most likely the same bug that several people have reported. Have you
patched the latest bugfixes for Ambertool? Is this AmberTool 1.4?
All the best,
Ray
On Tue, Jul 26, 2011 at 3:18 PM, Roman Osman <roman.osman.mssm.edu> wrote:
> 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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> AMBER.ambermd.org
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>
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Received on Tue Jul 26 2011 - 15:30:04 PDT
