Hi All!
I generated 100 snapshots per rec/lig/complex for my prtien-ligand
system(from the unsolvated prmtop files and stripped mdcrd trajectory file).
Cross-checked the crd files by converting them back to pdb files. When I
proceed to the next step of calculating the binding free energy, the
mm_pbsa.in is a copy of the one in the example folder with neccessary
changes made. On $AMBERHOME/exe/mm_pbsa.pl mm_pbsa.in > binding.log &
I get the following:
*Missing values for MM ELE
*
The log file is as follows: I am sure that the mdcrd file is stripped off
water and ions and the prmtop files are unsolvated. On cross-checking with
the example files in the src/mm_pbsa/Examples folder, it found that the
output in my case looks different after ' Calculating energy /entropy ...'
seems like the program is not doing any calculations at all with my
input/snapshots. Also, the example .pl script works fine. What am I doing
wrong?
=>> Reading input parameters
Found PREFIX => 1nfu_binding
Found PATH => snapshots/
Found COMPLEX => 1
Found RECEPTOR => 1
Found LIGAND => 1
Found COMPT => 1nfu_lig_complex.prmtop
Found RECPT => 1nfu_ca_only.prmtop
Found LIGPT => 1nfu_lig.prmtop
Found =>
Found GC => 0
Found AS => 0
Found DC => 0
Found MM => 1
Found GB => 1
Found PB => 1
Found MS => 1
Found NM => 1
Found PROC => 2
Found REFE => 0
Found INDI => 1.0
Found EXDI => 80.0
Found SCALE => 2.0
Found LINIT => 1000
Found PRBRAD => 1.4
Found RADIOPT => 0
Found SURFTEN => 0.00542
Found SURFOFF => 0.92
Found DIELC => 1.0
Found IGB => 2
Found GBSA => 1
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 DIELC => 4
Found MAXCYC => 1000
Found DRMS => 0.1
=>> Checking sanity
Checking GENERAL
Checking MM
Checking NM
Checking PB
Checking GB
Checking MS
=>> Creating input
Sander input
PBSA 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 = 0.00
=>> Reading input
=>> Reordering files
Final order:
1. 1nfu_binding_com.all.out: -
2. 1nfu_binding_rec.all.out: -
3. 1nfu_binding_lig.all.out: -
=>> Reading files
Reading 1nfu_binding_com.all.out
Reading 1nfu_binding_rec.all.out
Reading 1nfu_binding_lig.all.out
=>> Treat special parameters
=>> Calc missing parameters
Processing MM ELE
Processing MM GAS
Processing MM INT
Processing MM VDW
Processing GB GBTOT
Processing GB GBELE
Processing GB GBSOL
Processing PB PBSOL
Processing PB PBELE
Processing PB PBTOT
=>> Calc delta from raw data
Any help will be much appreciated.
Thanks
Rima
--
-Rima
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Received on Sun Feb 11 2007 - 06:07:11 PST
