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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Received on Thu Jan 26 2006 - 06:10:07 PST
