AMBER Archive (2005)

Subject: AMBER: mm_pbsa problem

From: emilia wu (emiliawu_at_dicp.ac.cn)
Date: Mon Oct 31 2005 - 20:53:51 CST

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_at_dicp.ac.cn
　　　　　　　　　　2005-11-01






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