AMBER Archive (2005)

Subject: AMBER: normal mode mm/pbsa interupted

From: Eric Hu (eric.y.hu_at_gmail.com)
Date: Thu Jun 09 2005 - 13:46:04 CDT

Hi, I am running a Amber 8 mm/pbsa job to evaluate the entropy of a
small molecule with a protein. The enthalpy calculations are executed
normally. The calculation of substrate-receptor complex is fine but
stopped at the 65th of the receptor with the following errors
(sanmin_rec.65.out):

    4. RESULTS
------------------------------------------------------------------------
--------

  ---------------------------------------------------

      eedmeth=5: Using 1/r dielectric

  ---------------------------------------------------
  Frac coord min, max: 0.171586430945041 1.07391120669790
  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

The question is that why this happens since the all snapshots of the
complex (100) are carried through. Thank you for any suggestions.

Eric

######mm_pbsa.in########
@GENERAL
#
PREFIX pepB
PATH ../nm_pepB_snapshots/
#
COMPLEX 1
RECEPTOR 1
LIGAND 1
#
COMPT ../93f3_pepB.top
RECPT ../93f3.top
LIGPT ../pepB.top
#
GC 0
AS 0
DC 0
#
MM 0
GB 0
PB 0
MS 0
#
NM 1
#
########################################################################
########
@NM
#
DIELC 4
MAXCYC 1000
DRMS 0.1

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