Re: [AMBER] Excluded atoms list

From: Ross Walker <>
Date: Wed, 24 Nov 2010 16:24:57 -0800

Hi Jason,

AMBER silently rebuilds the excluded atom list inside extra_pts.f - This is
somewhat annoying but was a hack put in to support extra points. Try setting
chngmask=0 in the cntrl namelist. This 'should' prevent sander and pmemd
from rebuilding the exclusion list and so will use the one that is inside
the prmtop file.

Good luck,

> -----Original Message-----
> From: Jason S Grosch []
> Sent: Wednesday, November 24, 2010 2:42 PM
> To:
> Subject: [AMBER] Excluded atoms list
> Hello,
> I'm attempting to alter specific molecular interactions such that some
> from different residues do not interact via charges or Lennard-Jones. I
> thought that altering the excluded atoms list in the topology file would
> the way to accomplish this, but regardless of what I do to the excluded
> list, keeping the number of excluded atoms list consistent, the energy is
> always the same. For example: running a simulation with two CO2 molecules
> with all atoms excluded has exactly the same energy as the unadjusted
> topology file. The only difference between the two md.out files is ~ 1kb
> allocated memory. Does the excluded atoms list do anything? There is
> information on this. Also, if this is not the way to remove specific
charge and
> LJ interactions, is this possible to do?
> Any assistance appreciated,
> Jason Grosch
> _______________________________________________
> AMBER mailing list

AMBER mailing list
Received on Wed Nov 24 2010 - 16:30:05 PST
Custom Search