AMBER Archive (2004)

Subject: AMBER: found unknown atflg PB

From: Scott (spendley_at_uofu.net)
Date: Thu Jul 22 2004 - 08:38:33 CDT

I am attempting to execute mm_pbsa for the first time using amber 8 and
I keep running into this error. It would appear not to recognize the
flag for the PB section although when looking in the log file, the
program has read in the first variable of that section. Has anyone run
into this error before? Thank you in advance.

Scott

My input and log file are attached below.


=>> Init data
    Presuming executables of amber suite to be in /local/src/AMBER/amber8/exe

=>> Reading input parameters
    Found PREFIX => Tir.ES
    Found PATH => /local/people/pendley/PBSA
    Found COMPLEX => 0
    Found RECEPTOR => 1
    Found LIGAND => 0
    Found RECPT => /local/people/pendley/PBSA/Tir.ES.parm
    Found GC => 1
    Found AS => 0
    Found DC => 0
    Found MM => 1
    Found GB => 0
    Found PB => 1
    Found MS => 1
    Found NM => 0
    Found PROC => 2


@GENERAL
#
PREFIX Tir.ES
PATH /local/people/pendley/PBSA
#
COMPLEX 0
RECEPTOR 1
LIGAND 0
#
RECPT /local/people/pendley/PBSA/Tir.ES.parm
#
GC 1
AS 0
DC 0
#
MM 1
GB 0
PB 1
MS 1
NM 0
#
#############################################################################
@PB
#
PROC 2
REFE 0
INDI 1.0
EXDI 80.0
SCALE 10
LINIT 1000
PRBRAD 1.6
#
RADIOPT 1
#
FOCUS 0
PERFIL 80.0
CHARGE /local/src/AMBER/amber8/src/mm_pbsa/Examples/my_amber94_delphi.crg
SIZE /local/src/AMBER/amber8/src/mm_pbsa/Examples/my_parse_delphi.siz
#
SURFTEN 0.005
SURFOFF 0.0
#
@MM
#
DIELC 1.0
###############################################################################
@MS
#
PROBE 0.0
##########################################################################
@NM
DIELC 4
MAXCYC 1000
DRMS 0.0001
##############################################################################
@MAKECRD
#
BOX YES
NTOTAL 21697
NSTART 1
NSTOP 58
NFREQ 1
#
NUMBER_LIG_GROUPS 0
LSTART 0
LSTOP 0
NUMBER_REC_GROUPS 1
RSTART 1
RSTOP 1076
#############################################################################
@TRAJECTORY
TRAJECTORY /local/people/pendley/PBSA/Tir.ES.pbsa2.x
############################################################################
@PROGRAMS
#
DELPHI /local/src/delphi/irix/exe/delphi

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