Re: [AMBER] .rst7 output coordinate file error

From: David A Case <>
Date: Wed, 23 Jun 2021 08:34:22 -0400

On Tue, Jun 22, 2021, GALLO FACUNDO NAHUEL wrote:

>Hi! I'm having trouble when running a ligand-protein MD simulation. For
>one specific ligand, when I run the first equilibration (eqv) the .rst7
>coordinate file is nonsense. The same .mdin equilibration file works for
>all the other ligands in the same system, and the coordinates in the .rst7
>files are correctly written, so it seems to be something wrong with the
>ligand. The .mdin used is:
> NTPR=20000 NSTLIM=100000,DT=0.0001,NRESPA=1 ,

First, try setting nstlim=100 and ntpr=1. Study the energies in the output
file. Slowly increase the number of steps if the problem does not occur
right away. And, try using the checkstructure
action in cpptraj. There are probably bad contacts or a bad force field
involved here.

Second, why are you using dt=0.0001? That is about ten times smaller than
usual. If you find you need that small a time step for other ligands,
something untoward is going on.

>The .out file doesn't show any error ...

Do the energies make sense? It's not clear what you mean by "doesn't show
any error". It's possible for the molecules to get very large
coordinates (so the the rst7 file overflows), but still have all the
internal geomtries be OK. But I can't recall every seeing such behavior


AMBER mailing list
Received on Wed Jun 23 2021 - 06:00:02 PDT
Custom Search