Hello,
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
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
quit
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sun Jul 04 2010 - 05:30:03 PDT
