AMBER Archive (2004)

Subject: AMBER: mm_pbsa test problem

From: Difei Wang (
Date: Wed Jun 02 2004 - 10:54:40 CDT

Dear All,

I am testing the examples for mm_pbsa in Amber7 under PC linux cluster system.
The example files are located in $AMBERHOME/amber7/src/mm_pbsa/Examples/.
When I tried the test, it run correctly for "01_GenerateSnapshots", "02_MMPBSA_Stability"
"03_MMPBSA_Binding", "05_MMPBSA_Decomp_Residue", "06_MMPBSA_Decomp_Pair"
but not for "04_MMPBSA_Nmode".

It seems like a nmode problem. But when I tried the test examples in
$AMBERHOME/amber7/test/nmode. Nmode works fine.

Could someone help me to figure out what happened? I searched Amber archives.
But no one had this problem.



BTW: I found you can comment line710 "print OUT " ntxo = 0,\n";" if you want
have ASCII format of the restart file in "04_MMPBSA_Nmode". But it doesn't help

Here is the error message in mm_pbsa.log

=>> Init data
    Presuming executables of amber suite to be in /opt/amber7/exe

=>> Reading input parameters
    Found PREFIX => ras_raf_II_wt
    Found PATH => ../01_GenerateSnapshots/
    Found COMPLEX => 0
    Found RECEPTOR => 0
    Found LIGAND => 1
    Found COMPT => ../ras_raf_II_wt.prmtop
    Found RECPT => ../ras_II_wt.prmtop
    Found LIGPT => ../raf_wt.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 => 5000
    Found DRMS => 0.1
    Found DELPHI => /opt/delphi/bin/delphi

=>> Checking sanity
    Checking GENERAL
    Checking NM

=>> Creating input
    Nmode input
=>> Calculating energy / entropy contributions
    Calc contrib for ../01_GenerateSnapshots/ras_raf_II_wt_lig.crd.1
        Minimize structure
        Calc entropy

** Address Error **

End of diagnostics

        /home/fs/wiest/dwang/bin/amber7/exe/nmode -O -i -o nmode_lig.1.out -c sanmin
_lig.1.restrt -p ../raf_wt.prmtop not running properly


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