Hi,
> this process: 21890 atoms, partner process: 23383 atoms
> SANDER BOMB in subroutine setup_sc
> All non-softcore atoms must be identical in both systems
[...]
> Since number of Na ions for neutrality of the both systems is the same,
> this difference in number of atoms corresponds to water molecules.
You cannot build the two end states independently. All atoms, except the
ones in your scmasks must be identical in their starting positions and
order in the prmtop. It may be easiest to built a single pdb-file of your
system with water and ions and read it into leap twice, just changing the
residue name or something similar to build V0 and V1.
Thomas
Dr. Thomas Steinbrecher
formerly at the
BioMaps Institute
Rutgers University
610 Taylor Rd.
Piscataway, NJ 08854
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Received on Sun Feb 19 2012 - 05:30:02 PST
