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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Received on Tue May 10 2011 - 13:30:05 PDT
