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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Received on Wed May 04 2005 - 19:53:00 PDT
