Dear Amber users,
I'm trying to run MM_PBSA in Amber 8 to calculate entropy. I get the following error message:
"Can't use an undefined value as an ARRAY reference at /export/home/wl/amber8/src/mm_pbsa/mm_pbsa_statistics.pm line 903. "
I don't know if this is due to something I input or if there is some
other problem. My input and ouput are shown below.
----------------------------------
mm_pbsa.in:
.GENERAL
PREFIX thrombin_osc_wat
PATH ./snapshot/
COMPLEX 1
RECEPTOR 1
LIGAND 1
#
COMPT ./carnal/comp.prmtop
RECPT ./carnal/recpt.prmtop
LIGPT ./carnal/ligand.prmtop
#
GC 0
AS 0
DC 0
#
MM 0
GB 0
PB 0
MS 0
#
NM 1
#
.NM
DIELC 4
MAXCYC 1000000
DRMS 0.0001
-----------------------------------
mm_pbsa.log:
=>> Init data
Presuming executables of amber suite to be in /export/home/wl/amber8/exe
=>> Reading input parameters
Found PREFIX => thrombin_osc_wat
Found PATH => ./snapshot/
Found COMPLEX => 1
Found RECEPTOR => 1
Found LIGAND => 1
Found COMPT => ./carnal/comp.prmtop
Found RECPT => ./carnal/recpt.prmtop
Found LIGPT => ./carnal/ligand.prmtop
Found GC => 0
Found AS => 0
Found DC => 0
Found MM => 0
Found GB => 0
Found PB => 0
Found MS => 0
Found NM => 1
Found DIELC => 4
Found MAXCYC => 1000000
Found DRMS => 0.0001
Found DELPHI => /home/gohlke/src/delphi.98/exe/delphi
=>> Checking sanity
Checking GENERAL
Checking NM
=>> Creating input
Nmode input
=>> Calculating energy / entropy contributions
=>> Doing statistics
=>> Values of global variables
TEMP = 300
R = 8.314
gammaP = 0.00542
betaP = 0.92
gammaG = 0.0072
betaG = 0
=>> Reading input
=>> Reordering files
Final order:
1. thrombin_osc_wat_com.all.out: -
2. thrombin_osc_wat_rec.all.out: -
3. thrombin_osc_wat_lig.all.out: -
=>> Reading files
Reading thrombin_osc_wat_com.all.out
Reading thrombin_osc_wat_rec.all.out
Reading thrombin_osc_wat_lig.all.out
=>> Treat special parameters
=>> Calc missing parameters
=>> Calc delta from raw data
----------------------------------------
The attatchments are the produced files by mm_pbsa.pl
Any help would be greatly appreciated!
Thanks a lot in advance.
Best Regards,
emilia
emiliawu.dicp.ac.cn
2005-11-01
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Received on Tue Nov 01 2005 - 03:53:00 PST
