Hallo,
I 'm trying to calculate the binding enrgy of a ligand to
a protein using ANAL.
Therefor I created the following configuration file, which I basically
copied from a former Mailing :
TITLE 'Test'
1 0 0 0 20 1
0 51.4828921 39.7147560 57.5269096 90.0
7 0 1 0 50 1
12.0 .0 1.2 4.0
1 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0
IOPT 'ENERGY'
protein
RES 1 277
END
ligand
RES 278-279
END
END
STOP
If I start AMBER I only get the following output :
---------------------------------------------------------------
Amber 5.0 ANAL: Static Analysis for Energy/Structure UCSF 1997
---------------------------------------------------------------
1. RESOURCE USE:
| INFO: Old style PARM file read
Memory Use Allocated Used
Real 500000 73027
Integer 800000 149048 (static)
Max Nonbonded Pairs: 650952 packed 1 to a machine word
2. DATA CONTROL:
TITLE 'Test'
NTX = 1 NTXO = 0 NRC = 0
NRCX = 0 NGRPX = 20 KFORM = 1
NTB = 0 BOXX = 51.483 BOXY = 39.715
BOXZ = 57.527 BETA = 90.000
NTF = 7 NTID = 0 NTN = 1
NTNB = 0 NSNB = 50 IDIEL = 1
RCUT = 12.00 SCNB = 2.00
SCEE = 1.20 DIELC = 4.00
IMAX EBMAX EANMAX EDIHMAX ENB14MAX
1 0.00 0.00 0.00 0.00
EEL14MAX ENBMAX EELMAX EHBMAX ECONSMAX
0.00 0.00 0.00 0.00 0.00
3. A T O M I C C O O R D I N A T E S
mod2
NUMBER OF ATOMS = 3992
But I don't get any calculations.
Does anyone know what could be wrong ?
Since I don't get any Error I don't know what to change.
Could it be a problem with the box ?
Hope someone can help..
Best wishes,
Daniel Wetzler
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Received on Fri Oct 08 2004 - 09:53:00 PDT
