AMBER Archive (2008)

Subject: AMBER: Error when performing Alanine scanning

From: Khaled Barakat (kbarakat_at_phys.ualberta.ca)
Date: Mon Jul 14 2008 - 20:41:26 CDT

Hello,

I am trying to use MM_PBSA to perform alanine scanning for a complex formed by two proteins.
below is my input file. when I try to run it I got the following error:

Param BOX does not exist

khaled

The input file:

PREFIX prot1-prot2
PATH ../01_GenerateSnapshots/
#
COMPLEX 1
RECEPTOR 1
LIGAND 1
#
COMPT ../complex.prmtop
RECPT ../prot1.prmtop
LIGPT ../prot2.prmtop
#
GC 0
AS 1
DC 0
#
MM 1
GB 1
PB 1
MS 1
#
NM 0
#
##############################################################################
##
@PB
#
# PB parameters (this section is only relevant if PB = 1 above)

PROC 2
REFE 0
INDI 1.0
EXDI 80.0
SCALE 2.0
LINIT 500
PRBRAD 1.6
#
RADIOPT 1
#
FOCUS 0
PERFIL 80.0
CHARGE ./my_amber94_delphi.crg
SIZE ./my_parse_delphi.siz
#
SURFTEN 0.005
SURFOFF 0.0
#
##############################################################################
##
@MM
#

#
DIELC 1.0
#
##############################################################################
##
@GB
#
 #
IGB 2
GBSA 2
SALTCON 0.00
EXTDIEL 80.0
INTDIEL 1.0
#
SURFTEN 0.0072
SURFOFF 0.00
#
##############################################################################
##
@MS
#

PROBE 0.0
#
@ALASCAN
#

NUMBER_MUTANT_GROUPS 1
MUTANT_ATOM1 1260
MUTANT_ATOM2 0
MUTANT_KEEP 1266
MUTANT_REFERENCE 1270

#

##############################################################################
###
@PROGRAMS
#
# Program executables
#
DELPHI /home/gohlke/src/delphi.98/exe/delphi
#
##############################################################################
##

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