AMBER Archive (2007)

Subject: RE: AMBER: mm-pbsa error with nm = 1

From: Hayden Eastwood (s0237717_at_sms.ed.ac.uk)
Date: Wed May 02 2007 - 06:10:10 CDT

 
Dear Cenk

The error message was obtained regardless of whether I used the test file
examples (amber9/src/mm-pbsa/Examples/04_MMPBSA_Nmode/mm_pbsa.in) or my own
input file. In both cases I get a crash when both NM and MM = 1). The
appended input files were used and I varied the values of NM and MM in each
one.

Many thanks for your help

hayden

Example input from amber (adjusted to fit my system for parm and crd files
only):
*****************************************************************8
@GENERAL
PREFIX snapshot
PATH ./
#
COMPLEX 1
RECEPTOR 1
LIGAND 1
#
COMPT ./HBD1_2SU.parm
RECPT ./HBD1.parm
LIGPT ./2SU.parm
#
GC 0
AS 0
DC 0
#
MM 0
&MM
DIELC 1.0
GB 0
PB 0
MS 0
#
NM 1
#
@NM
DIELC 4
MAXCYC 1000
DRMS 0.1
**********************************************************

My input file:
**********************************************************

@GENERAL
PREFIX snapshot
PATH ./
COMPLEX 1
RECEPTOR 1
LIGAND 1
COMPT ./HBD1_2SU.parm
RECPT ./HBD1.parm
LIGPT ./2SU.parm
GC 0
AS 0
DC 0
MM 0
GB 0
PB 0
MS 0
NM 1

@PB
PROC 2
REFE 0
INDI 1.0
EXDI 80.0
SCALE 2
LINIT 1000
PRBRAD 1.4
ISTRNG 0.0
RADIOPT 0
NPOPT 1
CAVITY_SURFTEN 0.0072
CAVITY_OFFSET 0.00
SURFTEN 0.0072
SURFOFF 0.00
@NM
DIELEC 4
MAXCYC 100000
DRMS 0.0001

@GB
IGB 2
GBSA 1
SALTCON 0.00
EXTDIEL 80.0
INTDIEL 1.0
SURFTEN 0.0072
SURFOFF 0.00

@MS
PROBE 0.0

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu