Hi Kirsten,
The problem is that one (probably more than one) coordinate for your two
systems for atoms that are not part of the softcore region are too
different. The atom names and numbers are not used to match atoms from the
two systems, only the order and scmask are used here.
Check coordinate 384 (i.e. x for atom 129) on both systems, either they
should be for common atoms, or on one side it should be in scmask.
If you want, sent me a copy of your setup (me, not the list) if it still
causes problems.
Kind Regards,
Thomas
> I have a problem with the thermodynamic integration.
> I work with amber10 bugfix32_12.
> Like tutorial A9 I have designed my PDB-files.
> I want to mutate DNA so I have a different number of atoms.
> So I have renamed the atom-number so that all atoms, that are
> equal in both files have the same atom number.
> Then I read in the PDB-files with the leap_2.in file
> and create the prm- and rst-files.
>
> But when I run the soft-core potential step my outputfile
> looked like this:
>
> " 3. ATOMIC COORDINATES AND VELOCITIES
> --------------------------------------------------------------------------------
>
>
> begin time read from input coords = 0.000 ps
>
> Number of triangulated 3-point waters found: 8428
> | Atom division among processors:
> | 0 27160
>
> Softcore Mask matches 0 atoms
> this run corresponds to V0, its softcore atoms interact fully for
> lambda=0
> this process: 27160 atoms, partner process: 27160 atoms
> Checking for mismatched coordinates.
> WARNING: Local coordinate 382 differs from partner coordinate
> 382 !
> Deviation is small, changing partner coordinate.
> WARNING: Local coordinate 383 differs from partner coordinate
> 383 !
> Deviation is small, changing partner coordinate.
> WARNING: Local coordinate 384 differs from partner coordinate
> 384 !
> SANDER BOMB in subroutine sc_check_and_adjust
> Atom coordinate disagreement
> Check input files. "
>
> When I crate PDB-files out of these prm- and rst-files,
> behind these atom numbers the atoms are different.
>
> So I don't know what I have done wrong,
> or how to fix this.
>
> Kind Regards
> Kirsten Heitmann
>
>
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>
Dr. Thomas Steinbrecher
BioMaps Institute
Rutgers University
610 Taylor Rd.
Piscataway, NJ 08854
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Received on Sun Jul 04 2010 - 08:00:03 PDT
