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
>>>
>>
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Received on Tue Jul 26 2011 - 16:00:02 PDT
