Dear Ben,
Just let me know if there is anything wrong in this method.
I am generating 50 structures for a template and as I told you program
crashed with 'Internal Error' message as 'Energy (= NaN)' value gone out
of the limits after generating 29 models. As you said to refine the
structure before modelling, but I couldn't find a direct method to do that
in inbuilt 'model' script, instead, I am generating 10 structures at a
time with different RAND_SEED value in each run, therefore running this 5
times (different RAND_SEED values) to get again 50 structures. Is this OK?
Yes, program runs fine. Please let me know, if there is any flaw in this
procedure as compared to a single run of generation of 50 structures.
I will be thankful.
thanks and regards,
Vivek Sharma
--------------------old message---------------
Date: Fri, 28 Jan 2005 19:12:59 +0200
From: vivek sharma <vivek.sharma(a)helsinki.fi>
Reply-To: vivek sharma <vivek.sharma(a)helsinki.fi>
Subject: problem
To: modeller_usage(a)salilab.org
Dear Sir,
I am a regular user of MODELER and I use 6v2.
But now when I was generating 50 structures of a target using some
templates, program ran fine till generating first 28 structures but died
in 29 structure generation with the error mentioned below (please see
below).
For, the first time I have observed this error. What can be the problem.
In the last statements of optimization schedule in log file you can see
the current value of energy is mentioned by 'NaN'. What does this mean,
looks like 'energy' has gone out of certain limits.
31 Non-bonded restraints : 1.0000
32 Atomic accessibility restraints : 1.0000
33 Atomic density restraints : 1.0000
Initial value of energy before optimization : 35818.9410
Current energy : NaN
Symmetry term within energy : 0.0000
Optimizer exit status : 1
Number of iterations : 1
Number of calls to energy function : 201
Number of updates of dynamic contacts : 1
Number of non-updates of dynamic contacts : 201
Final maximal atomic shift : 0.000
TOP_________> 7609 235 IF ARGUMENTS = WRITE_INTERMEDIATES 1, OPERATION
= 'EQ', ;
THEN = 'WRITE_MODEL FILE = default,
FILE_EXT = P;
DB_EXT, FILE_ID = .B'
TOP_________> 7610 236 IF ARGUMENTS = ERROR_STATUS 0, OPERATION
= 'GT', ;
THEN = 'GO_TO __ABORT'
TOP_________> 7611 237 IF ARGUMENTS = MOLPDF MAX_MOLPDF, OPERATION
= 'GT', ;
THEN = 'GO_TO __ABORT'
TOP_________> 7612 238 END_DO
TOP_________> 7613 232 OPERATE ARGUMENTS = ID1 1, OPERATION = 'SUM',
RESULT = ID;
1
TOP_________> 7614 233 PICK_RESTRAINTS ADD_RESTRAINTS = OFF
pick_re_612_> Number of MODEL atoms, selected restraints; 3854 49753
TOP_________> 7615 234 OPTIMIZE
getcell_247E> Internal error:
recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1
Dynamically allocated memory at finish [B,kB,MB]: 55660213
54355.680 53.082
Starting time : 2005/01/28
14:43:47.350
Closing time : 2005/01/28
18:09:34.578
Total CPU time [seconds] : 12315.51
Please have a look to the error, and suggest what can be the reason. I am
first time facing such strange error, otherwise MODELER has worked fine
always.
Regards,
Vivek
--
VIVEK SHARMA
"You must be the change you wish to see in the world."
MKG
----- End forwarded message -----
--
VIVEK SHARMA
HBG BI
"You must be the change you wish to see in the world."
MKG
