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-- Jason M. Swails Quantum Theory Project, University of Florida Ph.D. Candidate 352-392-4032 On Jul 26, 2011, at 6:36 PM, "Ray Luo, Ph.D." <ray.luo.uci.edu> wrote: > It doesn't hurt to install all the bugfixes ... make sure all the test > cases can pass before any new runs ... > > Ray > > On Tue, Jul 26, 2011 at 3:23 PM, Roman Osman <roman.osman.mssm.edu> wrote: >> No, this is AmberTool 1.5. >> Thanks, >> I'll ask our administrator to install the bugfixes, anyone in particular? >> Rami >> >> >> On 7/26/11 6:21 PM, "Ray Luo, Ph.D." <ray.luo.uci.edu> wrote: >> >>> 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 >>>> >>>> >>>> >>>> _______________________________________________ >>>> AMBER mailing list >>>> AMBER.ambermd.org >>>> http://lists.ambermd.org/mailman/listinfo/amber >>>> >>> >>> _______________________________________________ >>> AMBER mailing list >>> AMBER.ambermd.org >>> http://lists.ambermd.org/mailman/listinfo/amber >> >> >> _______________________________________________ >> AMBER mailing list >> AMBER.ambermd.org >> http://lists.ambermd.org/mailman/listinfo/amber >> > > _______________________________________________ > AMBER mailing list > AMBER.ambermd.org > http://lists.ambermd.org/mailman/listinfo/amber _______________________________________________ AMBER mailing list AMBER.ambermd.org http://lists.ambermd.org/mailman/listinfo/amberReceived on Tue Jul 26 2011 - 16:30:03 PDT