Hi Ray,
We reinstalled AmberTools 1.5 with all the bugfixes. The test suite passed
OK.
However, running MMPBSA.py I am getting an error:
PB Bomb in assignlvlset(): illegal insas flag 53 41 93 0
The PB section stops and MMPBSA continues next to calculate the normal
modes.
The input to the job and the script are the same as before (see below).
I might add that while in this system the error occurs always at the same
point, this error may not appear at all in a different trajectory or a
different system.
I hope someone could help.
Thanks very much,
Rami
On 7/26/11 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
>>>>
>>>>
>>>>
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>>>>
>>>
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Received on Fri Jul 29 2011 - 12:00:03 PDT
