Yes, I can do it, but don't you need a trajectory as well? It's about 480
MB.
I could try to upload it to a site that you can have access to.
I'll send another message when it's ready.
Thanks for your help.
Rami
On 7/29/11 6:51 PM, "Ray Luo, Ph.D." <ray.luo.uci.edu> wrote:
> I'm forwarding this to MJ to look over, can you send to me and MJ, off
> the list, a sample set of input file and prmtop file for the
> calculation?
>
> All the best,
> Ray
>
> On Fri, Jul 29, 2011 at 11:53 AM, Roman Osman <roman.osman.mssm.edu> wrote:
>> 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 Sat Jul 30 2011 - 11:30:03 PDT
