AMBER Archive (2006)

Subject: AMBER: MM-PBSA

From: Douali, Latifa (latifa.douali_at_pnl.gov)
Date: Wed Jan 25 2006 - 17:03:06 CST

Dear all,

I am trying to get the absolute free energy of a DNA dodecamer. So I ran
MD for my system with explicit water. I used ptraj to strip water from
my trajectory and to generate new mdcrd file. I used mm_pbsa to generate
snapshots. This part of the job was successful and I got the crd files.
When I tried to calculate the free energy, the calculation crashed
giving this error message:
"Died at /home/latifa/amber8/src/mm_pbsa/mm_pbsa_readinput.pm line 344."
And in the output (mm-pbsa.log) file I got this :

=>> Init data
    Presuming executables of amber suite to be in
/home/latifa/amber8/exe

=>> Reading input parameters
    Found PREFIX => twelvemerG_nonpert_nowat
    Found PATH => ../twelvemerG_nowater_snapshots/
    Found COMPLEX => 1
    Found RECEPTOR => 0
    Found LIGAND => 0
    Found COMPT => ../twelvemerG_nowater.prmtop
    Found RECPT => XXX
    Found LIGPT => XXX
    Found GC => 0
    Found AS => 0
    Found DC => 1
    Found MM => 1
    Found GB => 1
    Found PB => 0
    Found MS => 0
    Found NM => 0
    Found DIELC => 1.0
    Found IGB => 1
    Found GBSA => 2
    Found SALTCON => 0.00
    Found EXTDIEL => 80.0
    Found INTDIEL => 1.0
    Found SURFTEN => 0.0072
    Found SURFOFF => 0.00
    Found PROBE => 0.0
    Found DCTYPE => 2
    Found COMREC => 1-46
    Found COMLIG => XXX
    Found COMPRI => 18
    Found RECRES => XXX
    Found RECPRI => XXX
    Found RECMAP => XXX
    Found LIGRES => XXX
    Found LIGPRI => XXX
    Found LIGMAP => XXX
    Found DELPHI => /home/latifa/amber8/src/pbsa

=>> Checking sanity
    Checking GENERAL
    Implicit SAS calc by sander
    Cannot find directory ../twelvemerG_nowater_snapshots/
~

Here is a part of my mm-pbsa input file

PREFIX twelvemerG_nonpert_nowat
PATH ../twelvemerG_nowater_snapshots/
#
COMPLEX 1
RECEPTOR 0
LIGAND 0
#
COMPT ../twelvemerG_nowater.prmtop
RECPT XXX
LIGPT XXX
#
GC 0
AS 0
DC 0
#
MM 1
GB 1
PB 0
MS 0
#
NM 0
#
...

IGB 2
GBSA 1
SALTCON 0.00
EXTDIEL 80.0
INTDIEL 1.0
#
SURFTEN 0.0072
SURFOFF 0.00
#

...

@DECOMP
#
DCTYPE 2
#
##COMREC 1-46
##COMLIG XXX
##COMPRI 18
##RECRES XXX
##RECPRI XXX
##RECMAP XXX
##LIGRES XXX
##LIGPRI XXX
##LIGMAP XXX
###
########################################################################
########

@PROGRAMS
#
# Program executables
#
DELPHI /home/latifa/amber8/src/pbsa
#

Please could someone tell me what do I do wrong here

Thanks

Latifa

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