AMBER Archive (2007)

Subject: AMBER: System extending beyond of (non existent) virtual box

From: Francesco Pietra (chiendarret_at_yahoo.com)
Date: Fri Sep 07 2007 - 12:17:36 CDT

Consultation of the archive notwithstanding I am puzzled by the following
message at the end of minout:

   NSTEP ENERGY RMS GMAX NAME NUMBER
   3900 4.8716E+01 6.1030E-04 4.2568E-03 C 19

 BOND = 0.9194 ANGLE = 3.1885 DIHED = 25.0950
 VDWAALS = -3.3985 EEL = -17.5549 HBOND = 0.0000
 1-4 VDW = 7.8486 1-4 EEL = 32.6179 RESTRAINT = 0.0000

   NSTEP ENERGY RMS GMAX NAME NUMBER
   3950 4.8716E+01 2.0648E-04 1.0189E-03 C1 21

 BOND = 0.9194 ANGLE = 3.1885 DIHED = 25.0950
 VDWAALS = -3.3985 EEL = -17.5549 HBOND = 0.0000
 1-4 VDW = 7.8486 1-4 EEL = 32.6179 RESTRAINT = 0.0000

   NSTEP ENERGY RMS GMAX NAME NUMBER
   4000 4.8716E+01 1.5402E-04 4.4388E-04 H20 37

 BOND = 0.9194 ANGLE = 3.1884 DIHED = 25.0951
 VDWAALS = -3.3985 EEL = -17.5548 HBOND = 0.0000
 1-4 VDW = 7.8486 1-4 EEL = 32.6179 RESTRAINT = 0.0000
 Frac coord min, max: -2.60554141237325 3.54373637786288
 The system has extended beyond
     the extent of the virtual box.
 Restarting sander will recalculate
    a new virtual box with 30 Angstroms
    extra on each side, if there is a
    restart file for this configuration.
 SANDER BOMB in subroutine Routine: map_coords (ew_force.f)
 Atom out of bounds. If a restart has been written,
 restarting should resolve the error

minin:

Classical minimization in vacuum
&cntrl
imin=1, ncyc=4000, maxcyc=10000,
ntb=0, ntc=1, ntf=1,
cut=25
/

Identical error message with "cut=999".

The procedure was launched with

mpirun -np 1 $AMBERHOME/exe/sander.MPI, as it deals of a 39-atoms molecule,
single residue. I used before those inputs with a variety of molecules, bigger
and more complicated than present one. prepin was obtained with antechamber,
which recognized everything.

The molecule was carefully minimized with MMFF94 before input to antechamber,
and prmtop inpcrd give the correct structure. I can also add that the input pdb
could be minimized DFT with a number of functionals and basis set with no
problem.

In neither mpirun was a restart file produced, so that I can't check
graphically what happened, in particular what has moved apart in the molecule.
Though I feel that it must be a trivial problem, I am unable to come out.

Thanks for help.

francesco pietra

       
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