[AMBER] WARNING: Local coordinate 382 differs from partner coordinate 382 !

From: kirsten <kirstenheitmann.gmx.net>
Date: Sun, 04 Jul 2010 14:07:08 +0200


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:


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
     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

source leaprc.ff03
source leaprc.gaff

loadOff libs/znb.lib
loadAmberParams libs/frcmod.zinc

m0 = loadPdb m0_leap_out.pdb
setBox m0 vdw
savePdb m0 m0_sol_leap.pdb
saveAmberParm m0 m0.prm m0.rst

m18 = loadPdb m18_m0_leap_out.pdb
setBox m18 vdw
savePdb m18 m18_sol_leap.pdb
saveAmberParm m18 m18.prm m18.rst


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Received on Sun Jul 04 2010 - 05:30:03 PDT
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