On Thu, Dec 26, 2013 at 8:37 AM, Asfa Ali <asfa.iisc.gmail.com> wrote:
> Hi,
>
> I checked and found that the bond energies are missing in all the
> frames in snapshot_lig.all.out and also for snapshot_com.all.out
> (while snapshot_rec.all.out has bond energy in all the frames).
>
Something seems to be wrong with the topology file(s) and or their
compatibility with the input trajectories (that is usually what happens
when the energies are all *'s, especially bond energies).
> So I checked the lig_vac.prmtop, com_vac.prmtop and rec_vac.prmtop and
> found that the pdb structures formed by the above were fine (used
> ambpdb command).
>
You should visualize the topology files with some of the structures
generated by mm_pbsa.pl and look for any irregularities. Other than that
very general advice, I will really only be able to provide help with
MMPBSA.py, so I suggest that you try using that version instead.
Good luck,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Thu Dec 26 2013 - 19:00:02 PST
