Dear everyone,
We are trying to analyze a DNA protein complex with metals (iron and
zinc) with mm_pbsa.pl module of AMBER9.
We obtained the following error message:
id_torus(): Could not find torus for atoms 579 and 5639
Use of uninitialized value in multiplication (*) at /Users/pgarcin/
Program/amber9/src/mm_pbsa/mm_pbsa_statistics.pm line 1376.
Use of uninitialized value in multiplication (*) at /Users/pgarcin/
Program/amber9/src/mm_pbsa/mm_pbsa_statistics.pm line 1344.
Use of uninitialized value in multiplication (*) at /Users/pgarcin/
Program/amber9/src/mm_pbsa/mm_pbsa_statistics.pm line 1472.
Use of uninitialized value in multiplication (*) at /Users/pgarcin/
Program/amber9/src/mm_pbsa/mm_pbsa_statistics.pm line 1472.
Use of uninitialized value in multiplication (*) at /Users/pgarcin/
Program/amber9/src/mm_pbsa/mm_pbsa_statistics.pm line 1475.
Use of uninitialized value in multiplication (*) at /Users/pgarcin/
Program/amber9/src/mm_pbsa/mm_pbsa_statistics.pm line 1475.
The two atoms 579 and 5636 are correspond to the H3 of a THY (DNA)
and the HA of an ARG (protein) respectively.
The input mm_pbsa.in file is:
.GENERAL
#
PREFIX slr
PATH ../ssZF-01/
#
COMPLEX 1
RECEPTOR 0
LIGAND 0
#
COMPT ../ssZF-01/slr_com.top
RECPT XXX
LIGPT XXX
#
GC 0
AS 0
DC 0
#
MM 1
GB 1
PB 1
MS 1
#
NM 0
#
########################################################################
########
.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
#
########################################################################
########
.MM
#
DIELC 1.0
#
########################################################################
########
.GB
#
IGB 2
GBSA 1
SALTCON 0.00
EXTDIEL 80.0
INTDIEL 1.0
#
SURFTEN 0.0072
SURFOFF 0.00
#
########################################################################
########
.MS
#
PROBE 0.0
#
########################################################################
#########
.PROGRAMS
########################################################################
########
Does someone could give me some suggestions obout the error message?
Thanks for any help.
____________________
Yves BOULARD
CEA SACLAY
DSV/iBiTec-S/SBIGeM/LBI
Bat. 144 P.C. 22
91191 Gif-sur-Yvette Cedex
France
Tel: 33-1-69.08.35.84
Fax: 33-1-69.08.47.12
e-mail: yves.boulard.cea.fr
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Received on Wed Mar 14 2007 - 06:07:27 PDT
