2011/5/15 Andrew Voronkov <drugdesign.yandex.ru>
> 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?
>
The discussion of where/how to change fillratio in mm_pbsa.pl has been
mentioned several times in previous messages in the archive.
MMPBSA.py gives you direct access to this variable as an input in the &pb
namelist. Since that's the program that we know best here, we will be able
to help you more easily with that program.
All the best,
Jason
>
>
> 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>;
> >
> >> Maybe, i will try it, just want to figure out what the problem was.
> >>
> >> No I am getting another error:
> >> sander -O -i pbsa_com.in -o pbsa_com.2.out -c ./snapshot_com.crd.2 -p
> >> ./39798now.prmtop not successful
> >>
> >> while napshot_com.crd.1 was processed ok.
> >> Another thing is that I can get pdb from snapshot_com.crd.2 so prmtop
> fits
> >> to coordinates.
> >> $AMBERHOME/exe/ambpdb -p 39798now.prmtop <snapshot_com.crd.2>
> 39798now.pdb
> >> | New format PARM file being parsed.
> >> | Version = 1.000 Date = 05/08/11 Time = 14:53:33
> >>
> >> Just curious to get it working.
> >>
> >> Best regards,
> >> Andrew
> >>
> >> 11.05.2011, 00:14, "Jason Swails" <jason.swails.gmail.com>;:
> >>> It may be worth trying MMPBSA.py -- it automatically sets those
> >> parameters
> >>> in most cases and has a good deal of error/redundancy checks.
> >>>
> >>> All the best,
> >>> Jason
> >>>
> >>> 2011/5/10 Andrew Voronkov <drugdesign.yandex.ru>;;
> >>>> Hm, no actually it worked (btw it also works for ambpdb, it probably
> >> takes
> >>>> just one of the snapshots) and has shown that there is difference of
> >> number
> >>>> of atoms between prmtop and crd, but the solution was super simple.
> >> I've
> >>>> just used wrong ligand start and receptor start points.
> >>>>
> >>>> Best regards,
> >>>> Andrew
> >>>>
> >>>> 08.05.2011, 22:10, "Bill Ross" <ross.cgl.ucsf.EDU>;;:
> >>>>>> [voronkov.t60-2 36739]$ $AMBERHOME/exe/ambpdb -p 36739now.prmtop
> \
> >>>>>> <snapshot_com.crd.1> 36739-min1.pdb
> >>>>> Are you using an mdcrd file instead of a restrt? That won't work.
> >>>>>
> >>>>> Bill
> >>>>>
> >>>>> _______________________________________________
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> >>> --
> >>> Jason M. Swails
> >>> Quantum Theory Project,
> >>> University of Florida
> >>> Ph.D. Candidate
> >>> 352-392-4032
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> > --
> > Bill Miller III
> > Quantum Theory Project,
> > University of Florida
> > Ph.D. Graduate Student
> > 352-392-6715
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--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Sun May 15 2011 - 15:30:03 PDT
