Re: [AMBER] wrong?

From: <>
Date: Mon, 15 Mar 2010 04:49:54 -0400 (EDT)

As a wild guess, since you dont say anything about your system:

Does your protein contain disulfide-bonds and did you include them not
only in the solvated complex you ran the MD on, but also in the
postprocessing vacuum-prmtop files? Insanely high vdw terms can come from
precisely this...


On Mon, March 15, 2010 4:34 am, Hannes Loeffler wrote:
> Your bonded and vdW terms look very high. Are you sure that your
> topology files match exactly the respective trajectories? Look at
> the structures (not only at the first one of a trajectory) with a
> molecular viewer. If there is something wrong you will probably spot
> it very quickly.
> _______________________________________________
> AMBER mailing list

Dr. Thomas Steinbrecher
BioMaps Institute
Rutgers University
610 Taylor Rd.
Piscataway, NJ 08854

AMBER mailing list
Received on Mon Mar 15 2010 - 02:00:04 PDT
Custom Search