Hi all,
*Info:*
Amber 11
Ambertools 1.4
mm_pbsa.pl Last change: 16.01.2002
All tests past in mm_pbsa.pl and there were no errors during make install.
I have a mm_pbsa.pl calculation running on 1001 snapshots but it has frozen
right at the end. When I "top" mm_pbsa.pl is still running. Tailing the log
filegives this:
Calc contrib for ./pl_com.crd.998
Calc MM/GB/SAS
Calc PBSA
Analyzing 998
Ana MM/GB/SAS
Ana PBSA
Calc contrib for ./pl_com.crd.999
Calc MM/GB/SAS
Calc PBSA
Analyzing 999
Ana MM/GB/SAS
Ana PBSA
Calc contrib for ./pl_com.crd.1000
Calc MM/GB/SAS
Calc PBSA
Analyzing 1000
Ana MM/GB/SAS
Ana PBSA
ls -lart reveals:
635 Sep 22 19:03 pbsa_com.in
81881 Sep 23 03:48 restrt
55501716 Sep 23 03:48 pl_com.all.out
434 Sep 23 03:48 mdinfo
137561 Sep 23 03:48 LOG
So nothing has happened since then (7 hours), can't find any errors in these
files. tailing pl_com.all.out gives:
PB_BDC 109 8.859 -2.646 -5.006 -13.218 0.000
PB_BDC 110 8.082 -0.855 -7.877 -7.841 0.000
PB_BDC 111 6.441 -2.884 -11.269 -1.187 0.000
PB_BDC 112 9.865 -2.340 -13.257 -3.205 0.000
PB_BDC 113 6.269 -2.608 -8.184
I've found this in the archive:
"*Use of uninitialized value in concatenation (.) or string at
/amber/amber11/src/mm_pbsa/mm_pbsa_createinput.pm line 596.
Use of uninitialized value in concatenation (.) or string at
/amber/amber11/src/mm_pbsa/mm_pbsa_createinput.pm line 596.
Use of uninitialized value in concatenation (.) or string at
/amber/amber11/src/mm_pbsa/mm_pbsa_createinput.pm line 596.
/amber/amber11/bin/sander -O -i pbsa_com.in -o pbsa_com.1.out -c
./snapshot_com.crd.1 -p ./c_Q635A.prmtop not successful
For details see:
http://ambermd.org/Questions/mm_pbsa.html#pbsa_command_not_successful
If comment out the line:
596c596
< print OUT " ipb = ${ipb}, inp = ${inp}, dielc =
${dielc},\n";
*
*---
> #print OUT " ipb = ${ipb}, inp = ${inp}, dielc =
${dielc},\n";
the program start but at the last step of the complex energy calculation
the output is freeze but the job still running. "*
I had the same error about line 596 but fixed it (or so I thought) by
setting inp to 0 in my input file. Any other setting than 0 is incompatible
with PB decomp.
Any help/suggestions for things to try would be great.
My mm_pbsa.in file:
.GENERAL
PREFIX pl
PATH ./
COMPLEX 1
RECEPTOR 1
LIGAND 1
COMPT ./pl_com.top.0
RECPT ./rec.top
LIGPT ./lig.top
GC 0
AS 0
DC 1
MM 1
GB 1
PB 1
MS 0
NM 0
###############################
.PB
PROC 2
REFE 0
INDI 1.0
EXDI 80.0
SCALE 2
LINIT 1002
PRBRAD 1.4
ISTRNG 0.0
RADIOPT 2
INP 0
NPOPT 1
CAVITY_SURFTEN 0.0072
CAVITY_OFFSET 0.00
SURFTEN 0.0072
SURFOFF 0.00
SALTCON 0.005
##################################
.DECOMP
DCTYPE 2
COMREC 1-144
COMLIG 145-148
COMPRI 1-148
RECRES 1-144
RECPRI 1-144
RECMAP 1-144
LIGRES 1-4
LIGPRI 1-4
LIGMAP 145-148
##############################
.MM
DIELC 1.0
.GB
IGB 1
GBSA 2
SALTCON 0.00
EXTDIEL 80.0
INTDIEL 1.0
SURFTEN 0.0072
SURFOFF 0.00
#################################
.MS
PROBE 0.0
#################################
.PROGRAMS
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Received on Thu Sep 23 2010 - 13:00:04 PDT
