ADL: Energy is Infinite error

Steve Madden smadden at cumbrepharma.com
Fri Mar 14 13:30:47 PDT 2008


Try reducing your grid size and see if that helps. 

I experienced a similar problem on running on Windows XP a few weeks
ago.  In my case it appears that setting the grid size to anything
greater than or equal to 64,64,64 (which default to 65,65,65 in windows)
resulted in getting these errors sporadically (some ga_runs not others)
in the dlg file and sometimes crashing the entire run with an error
(assertion "finite(avg)" failed: file "gs.cc").  I modified the grid
size to 63,63,63 (no other changes were made) and have run several
dockings with the same ligand and receptor and the error has not
reoccurred. 

Steve



-----Original Message-----
From: autodock-bounces at scripps.edu [mailto:autodock-bounces at scripps.edu]
On Behalf Of Raja S
Sent: Thursday, March 13, 2008 2:32 PM
To: autodock at scripps.edu
Subject: ADL: Energy is Infinite error


Hi all,
 
I am working on a docking with  these parameters:  normal LGA
parameters.
 
When I run autodock ( I am running Autodock tools on windows), i get
this error,:
 
Run: 1 / 10Date: Thu Mar 13 11:51:29 2008Output level is set to 1.
Creating an initial population of 150 individuals.
Assigning a random translation, a random orientation and 9 random
torsions to each of the 150 individuals.
Beginning Lamarckian Genetic Algorithm (LGA), with a maximum of
25000000energy evaluations.
Generation: 100   Oldest's energy: -52733758.880    Lowest energy:
-52733758.880    Num.evals.: 76867   Timing: Real= 0.03s,  CPU= 0.03s,
System= 0.00sGeneration: 200   Oldest's energy: -51643823.099    Lowest
energy: -54165430.825    Num.evals.: 143521   Timing: Real= 0.03s,  CPU=
0.03s,  System= 0.00seval.cc:  ERROR!  energy is infinite!
ATOM      1  C   INF     1      10.066  -5.620  13.315 +0.00 +0.00
+0.117ATOM      2  C   INF     1       9.510  -6.747  12.484 +0.00 +0.00
+0.214ATOM      3  C   INF     1       8.690  -6.480  11.448 +0.00 +0.00
-0.349ATOM      4  C   INF     1       9.801  -7.895  12.746 +0.00 +0.00
-0.274ATOM      5  C   INF     1       8.456  -5.562  11.238 +0.00 +0.00
+0.163ATOM      6  C   INF     1       8.149  -7.576  10.640 +0.00 +0.00
+0.172ATOM      7  C   INF     1       7.681  -8.707  11.558 +0.00 +0.00
+0.295ATOM      8  C   INF     1       8.772  -9.167  12.354 +0.00 +0.00
-0.348ATOM      9  C   INF     1       9.705  -9.800  11.481 +0.00 +0.00
+0.180ATOM     10  C   INF     1      10.339  -8.760  10.556 +0.00 +0.00
+0.194ATOM     11  C   INF     1       9.241  -8.111   9.705 +0.00 +0.00
+0.191ATOM     12  C   INF     1       6.624  -8.218  12.425 +0.00 +0.00
-0.288ATOM     13  C   INF     1       5.846  -7.198  12.026 +0.00 +0.00
+0.257A!
 
 TOM     14  C   INF     1       6.204  -6.416  10.788 +0.00 +0.00
+0.126ATOM     15  C   INF     1       4.860  -6.908  12.659 +0.00 +0.00
-0.266ATOM     16  C   INF     1      10.798 -10.478  12.310 +0.00 +0.00
+0.198ATOM     17  C   INF     1      10.792 -11.883  12.049 +0.00 +0.00
-0.398ATOM     18  C   INF     1      10.862 -12.326  12.906 +0.00 +0.00
+0.209ATOM     19  C   INF     1      11.002  -7.742  11.352 +0.00 +0.00
-0.311ATOM     20  C   INF     1      11.934  -6.954  10.794 +0.00 +0.00
+0.255ATOM     21  C   INF     1      13.332  -7.476  10.581 +0.00 +0.00
+0.126ATOM     22  C   INF     1      11.652  -5.827  10.463 +0.00 +0.00
-0.266ATOM     23  C   INF     1       9.803  -7.016   8.935 +0.00 +0.00
-0.311ATOM     24  C   INF     1      10.742  -7.260   8.009 +0.00 +0.00
+0.255ATOM     25  C   INF     1      10.468  -6.956   6.559 +0.00 +0.00
+0.126ATOM     26  C   INF     1      11.808  -7.725   8.337 +0.00 +0.00
-0.266e!
 
 val.cc:  ERROR!  energy is not a number!
ATOM      1  C   NaN     1      10.066  -5.620  13.315 +0.00 +0.00
+0.117ATOM      2  C   NaN     1       9.510  -6.747  12.484 +0.00 +0.00
+0.214ATOM      3  C   NaN     1       8.690  -6.480  11.448 +0.00 +0.00
-0.349ATOM      4  C   NaN     1       9.801  -7.895  12.746 +0.00 +0.00
-0.274ATOM      5  C   NaN     1       8.456  -5.562  11.238 +0.00 +0.00
+0.163ATOM      6  C   NaN     1       8.149  -7.576  10.640 +0.00 +0.00
+0.172ATOM      7  C   NaN     1       7.681  -8.707  11.558 +0.00 +0.00
+0.295ATOM      8  C   NaN     1       8.772  -9.167  12.354 +0.00 +0.00
-0.348ATOM      9  C   NaN     1       9.705  -9.800  11.481 +0.00 +0.00
+0.180ATOM     10  C   NaN     1      10.339  -8.760  10.556 +0.00 +0.00
+0.194ATOM     11  C   NaN     1       9.241  -8.111   9.705 +0.00 +0.00
+0.191ATOM     12  C   NaN     1       6.624  -8.218  12.425 +0.00 +0.00
-0.288ATOM     13  C   NaN     1       5.846  -7.198  12.026 +0.00 +0.00
+0.257A!
 
 TOM     14  C   NaN     1       6.204  -6.416  10.788 +0.00 +0.00
+0.126ATOM     15  C   NaN     1       4.860  -6.908  12.659 +0.00 +0.00
-0.266ATOM     16  C   NaN     1      10.798 -10.478  12.310 +0.00 +0.00
+0.198ATOM     17  C   NaN     1      10.792 -11.883  12.049 +0.00 +0.00
-0.398ATOM     18  C   NaN     1      10.862 -12.326  12.906 +0.00 +0.00
+0.209ATOM     19  C   NaN     1      11.002  -7.742  11.352 +0.00 +0.00
-0.311ATOM     20  C   NaN     1      11.934  -6.954  10.794 +0.00 +0.00
+0.255ATOM     21  C   NaN     1      13.332  -7.476  10.581 +0.00 +0.00
+0.126ATOM     22  C   NaN     1      11.652  -5.827  10.463 +0.00 +0.00
-0.266ATOM     23  C   NaN     1       9.803  -7.016   8.935 +0.00 +0.00
-0.311ATOM     24  C   NaN     1      10.742  -7.260   8.009 +0.00 +0.00
+0.255ATOM     25  C   NaN     1      10.468  -6.956   6.559 +0.00 +0.00
+0.126ATOM     26  C   NaN     1      11.808  -7.725   8.337 +0.00 +0.00
-0.266e!
 
 val.cc:  ERROR!  energy is infinite!
 
How do I go about solving the problem? i cannot seem to figure it out,
 
Raja
 
 
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