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
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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 - 09:30:03 PDT
