AMBER Archive (2006)

Subject: AMBER: one question about mm_pbsa

From: (duyongchun_at_mail.nankai.edu.cn)
Date: Thu Apr 13 2006 - 03:37:50 CDT


hi,Amber,
    I use mm_pbsa programe to compute binding energy.The mm_pbsa input file is as
flows:
#
################################################################################
@GENERAL
#
PREFIX ablpse
PATH ./
#
COMPLEX 1
RECEPTOR 1
LIGAND 1
#
COMPT ./ablpsenw.top
RECPT ./ablnw.top
LIGPT ./psenw.top
#
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 2.0
LINIT 500
PRBRAD 1.4
#
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 1
SALTCON 0.00
EXTDIEL 80.0
INTDIEL 1.0
#
SURFTEN 0.0072
SURFOFF 0.00
#
################################################################################
@MS
PROBE 0
#
################################################################################
@PROGRAMS
#
# Program executables
#
DELPHI /nfs/s07r2p1/phoebusdu/delphiexe/delphi
#
################################################################################

When I run ,it shows

Use of uninitialized value in hash element at
/nfs/s07r2p1/phoebusdu/amber8/amber8/src/mm_pbsa/mm_pbsa_readinput.pm line 260,
<IN> line 74.
Use of uninitialized value in hash element at
/nfs/s07r2p1/phoebusdu/amber8/amber8/src/mm_pbsa/mm_pbsa_readinput.pm line 260,
<IN> line 74.
Use of uninitialized value in multiplication (*) at
/nfs/s07r2p1/phoebusdu/amber8/amber8/src/mm_pbsa/mm_pbsa_statistics.pm line 1328.
Use of uninitialized value in multiplication (*) at
/nfs/s07r2p1/phoebusdu/amber8/amber8/src/mm_pbsa/mm_pbsa_statistics.pm line 1327.
Use of uninitialized value in multiplication (*) at
/nfs/s07r2p1/phoebusdu/amber8/amber8/src/mm_pbsa/mm_pbsa_statistics.pm line 1327.
Use of uninitialized value in multiplication (*) at
/nfs/s07r2p1/phoebusdu/amber8/amber8/src/mm_pbsa/mm_pbsa_statistics.pm line 1327.
    No data for 0+2 PB PB 0
and in the mm_pbsa log file it shows :
Reading ablpse_lig.all.out
    WARNING: Missing PB for PB in 0 -> Taken from -1
    WARNING: Missing PB for PB in 1 -> Taken from 0
    WARNING: Missing PB for PB in 2 -> Taken from 1
    WARNING: Missing PB for PB in 3 -> Taken from 2
Is there any body know why and how can I modify it?
Thanks!
 Yongchun Du
 2006.4.13

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