Hi Jason,
Thanks for your comment. For the purpose of different calculations, I first
remove all the ions and keep just 200 waters in the vicinity of the ligand
and binding pocket. I use the same trajectory for the MMPBSA and to compute
the water sites with our own program. Hence, the strip_mask of only waters.
Rami
On 7/26/11 7:23 PM, "Jason Swails" <jason.swails.gmail.com> wrote:
> Another comment -- I notice that you define your own strip_mask, which will
> only strip out water molecules. Do you have any ions in your system? Do you
> mean to leave these in there if you have them? If so, that may cause the
> error, since explicit ions are probably not parameterized frequently.
>
> Also, this leaving *all* ions intact makes it difficult to create consistent
> topologies.
>
> HTH,
> Jason
>
> --
> 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
>>>>>
>>>>
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Received on Tue Jul 26 2011 - 18:00:03 PDT
