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
>>
>
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Received on Tue Jul 26 2011 - 15:30:05 PDT
