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.
Thanks.
Difei
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
me.
Here is the error message in mm_pbsa.log
----BEGIN----
=>> 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 nmode_lig.in -o nmode_lig.1.out -c sanmin
_lig.1.restrt -p ../raf_wt.prmtop not running properly
-----END----
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Wed Jun 02 2004 - 17:53:01 PDT
