Re: [AMBER] Fwd:

From: Jason Swails <>
Date: Thu, 26 Dec 2013 21:33:01 -0500

On Thu, Dec 26, 2013 at 8:37 AM, Asfa Ali <> 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 and look for any irregularities. Other than that
very general advice, I will really only be able to provide help with, so I suggest that you try using that version instead.

Good luck,

Jason M. Swails
Rutgers University
Postdoctoral Researcher
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Received on Thu Dec 26 2013 - 19:00:02 PST
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