AMBER Archive (2005)

Subject: AMBER: mm/pbsa error

From: Eric Hu (eric.y.hu_at_gmail.com)
Date: Wed May 04 2005 - 13:06:34 CDT


Hi I ran into an error when doing nm calculation.

@GENERAL
PREFIX pepB
PATH ../nm_pepB_snapshots/
#
COMPLEX 1
RECEPTOR 1
LIGAND 1
#
COMPT ../ab_pepB.top
RECPT ../ab.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

The calculation stops at sanmin_rec.8.out with the following error:

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

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

     eedmeth=5: Using 1/r dielectric

 ---------------------------------------------------
  Frac coord min, max: 0.131100379560032 1.07346184405983
 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

If I understand correctly, sanmin_rec.in only does a local
minimization on the receptor (keep the conformation induced by the
ligand). Therefore there is a possibility that this receptor
is very unstable by itself. Is this why I get the error? If so, how do
I deal with it? Thanks.

Eric
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