Yes, I actually have taken a look and I have the same problem as described here ( pb_bomb in setgrd()):
http://structbio.vanderbilt.edu/archives/amber-archive/2009/0059.php
and here:
http://archive.ambermd.org/200408/0093.html
For now I have just requested to allocate more memory on cluster for my tasks, but if I will change
grid spacing (space=0.5), "fillratio" and "coarser "space" I should change it in mmpsa.pl script?
Best regards,
Andrew
15.05.2011, 20:21, "Bill Miller III" <brmilleriii.gmail.com>:
> Was there a more helpful error message written in the pbsa_com.2.out file?
>
> -Bill
>
> 2011/5/15 Andrew Voronkov <drugdesign.yandex.ru>;
>
>> šMaybe, i will try it, just want to figure out what the problem was.
>>
>> šNo I am getting another error:
>> šsander -O -i pbsa_com.in -o pbsa_com.2.out -c ./snapshot_com.crd.2 -p
>> š./39798now.prmtop not successful
>>
>> ššwhile napshot_com.crd.1 was processed ok.
>> šAnother thing is that I can get pdb from snapshot_com.crd.2 so prmtop fits
>> što coordinates.
>> šš$AMBERHOME/exe/ambpdb -p 39798now.prmtop <snapshot_com.crd.2> 39798now.pdb
>> š| New format PARM file being parsed.
>> š| Version = ššš1.000 Date = 05/08/11 Time = 14:53:33
>>
>> šJust curious to get it working.
>>
>> šBest regards,
>> šAndrew
>>
>> š11.05.2011, 00:14, "Jason Swails" <jason.swails.gmail.com>;:
>>> šIt may be worth trying MMPBSA.py -- it automatically sets those
>> šparameters
>>> šin most cases and has a good deal of error/redundancy checks.
>>>
>>> šAll the best,
>>> šJason
>>>
>>> š2011/5/10 Andrew Voronkov <drugdesign.yandex.ru>;;
>>>> ššHm, no actually it worked (btw it also works for ambpdb, it probably
>> štakes
>>>> ššjust one of the snapshots) and has shown that there is difference of
>> šnumber
>>>> ššof atoms between prmtop and crd, but the solution was super simple.
>> šI've
>>>> ššjust used wrong ligand start and receptor start points.
>>>>
>>>> ššBest regards,
>>>> ššAndrew
>>>>
>>>> šš08.05.2011, 22:10, "Bill Ross" <ross.cgl.ucsf.EDU>;;:
>>>>>> ššš[voronkov.t60-2 36739]$ $AMBERHOME/exe/ambpdb -p 36739now.prmtop \
>>>>>> ššš<snapshot_com.crd.1> 36739-min1.pdb
>>>>> ššAre you using an mdcrd file instead of a restrt? That won't work.
>>>>>
>>>>> ššBill
>>>>>
>>>>> šš_______________________________________________
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>>> š--
>>> šJason M. Swails
>>> šQuantum Theory Project,
>>> šUniversity of Florida
>>> šPh.D. Candidate
>>> š352-392-4032
>>> š_______________________________________________
>>> šAMBER mailing list
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>>> šhttp://lists.ambermd.org/mailman/listinfo/amber
>> š_______________________________________________
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> --
> Bill Miller III
> Quantum Theory Project,
> University of Florida
> Ph.D. Graduate Student
> 352-392-6715
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Received on Sun May 15 2011 - 15:00:02 PDT
