Hi Amber experts,
I am trying to run mm_pbsa.pl script to extract coordinates from the
trajectory but I keep getting this error message below, I do not know
whether or not it is something due to installation problem on our cluster
(IT support does not provide too much attention and always responds to our
emails one year later) or due to some problem in my script to run the job
(see below)
the command I use is
/export/home/nmonama/amber/bin/mm_pbsa.pl extract_coords.mmpbsa >
extract_coords.log
error is
Use of uninitialized value in concatenation (.) or string at
/export/home/nmonama/amber/bin/mm_pbsa.pl line 22.
Can't locate mm_pbsa_global.pm in .INC (.INC contains: /src/mm_pbsa
/usr/lib/perl5/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/5.8.8
/usr/lib/perl5/site_perl/5.8.8/x86_64-linux-thread-multi
/usr/lib/perl5/site_perl/5.8.8 /usr/lib/perl5/site_perl
/usr/lib/perl5/vendor_perl/5.8.8/x86_64-linux-thread-multi
/usr/lib/perl5/vendor_perl/5.8.8 /usr/lib/perl5/vendor_perl .) at
/export/home/nmonama/amber/bin/mm_pbsa.pl line 23.
BEGIN failed--compilation aborted at
/export/home/nmonama/amber/bin/mm_pbsa.pl line 23.
My input script is
.GENERAL
PREFIX snapshot
PATH ./
COMPLEX 1
RECEPTOR 1
LIGAND 1
COMPT ./com.top
RECPT ./rec.top
LIGPT ./lig.top
GC 1
AS 0
DC 0
MM 0
GB 0
PB 0
MS 0
NM 0
.MAKECRD
BOX YES
NTOTAL 20647
NSTART 1
NSTOP 100
NFREQ 1
NUMBER_LIG_GROUPS 1
LSTART 2772
LSTOP 2818
NUMBER_REC_GROUPS 1
RSTART 1
RSTOP 2771
.TRAJECTORY
TRAJECTORY ./5nsmd.mdcrd
.PROGRAMS
any help would be appreciated
best wishes
Mahmoud
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Received on Sat Apr 02 2011 - 12:00:02 PDT
