AMBER Archive (2009)

Subject: Re: [AMBER] Disappearing common atoms in Amber 10 with TI

From: steinbrt_at_rci.rutgers.edu
Date: Thu Jul 16 2009 - 09:09:39 CDT

Hi,

> I was trying to disappear/decouple a common atom using icfe=1, ifsc=0, and
> scmask, but that does not seem to work as I get zero in the vdW field of
> DV/DL averages. Does the scmask only work with soft core? If so, is there
> a way to set vdW parameters to zero in the input file or if not using
> xleap/tleap? Thanks,

scmask gives the mask of atoms experiencing soft-core potentials, it is
only read when the soft-core module is active (ifsc /= 0). If you do not
want to use the soft-core module (but I would recommend that you do), you
have to use dummy atoms in your end state. There might be an old tutorial
specifying how to do this, but I couldnt locate it.

Basically, you have to introduce a new atom type with zero vdW parameters
in place of whatever atom disappears. Depending on the nature of your
change, this can lead to severe convergence problems and might require
using klambda >=4.

Regards,

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

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