ADL: Re: trajectory output with AutoDock 3.05

Nataraj Balkrishnan natarajmtech at yahoo.co.uk
Fri Feb 11 01:54:13 PST 2005


Dear Autodockers,
                I am having docked  structures of ligands with a macromolecules. I want to see the
interaction of ligand functional group with the macromolecules such as Hydrogen bonds, hydrophobic interaction. Do you peoples know any freeware or script written by some one for 
this specific purpose? 
 
Kindly reply me.
 
Thank you in advance
 
B.Nataraj

mirosh <mirosh at ire.kharkov.ua> wrote:
Dear Maria and Stephan,

try to replace following lines in file src/autodock/main.cc:
line 1086 (void) sscanf( line, "%*s %1s", &selminpar ); 
replace on (void) sscanf( line, "%*s %c", &selminpar );

line 1226 (void) sscanf( line, "%*s %1s", &out_acc_rej );
replace on (void) sscanf( line, "%*s %c", &out_acc_rej );

Then you have just to recompile AutoDock. Hope this helps.

The corrected version of file main.cc is attached.

Best regards,
Kateryna Miroshnychenko,
Post graduate,
Institute of Radiophysics and Electronics,
National Academy of Sciences of Ukraine,
Kharkiv, Ukraine 




---------------------------------------------------------------------------------------------------------------------------------------------------
Dear Stephan,

seem to have the same trouble with AutoDock trajectories as you described in
this e-mail to the Autodock-mailing list.

Did you get an answer to your request at the time ??

Many thanks,

Maria Brandl
Globalphasing
Cambridge, UK

--------------------------------------------------------------------------------------------------------

I have problems to generate trajectory coordinates during an AutoDock 
run for every cycle.
For an example I set the following parameters in the docking parameter 
file:

runs 3 # number of runs
cycles 50 # cycles
accs 300 # steps accepted
rejs 300 # steps rejected
select m # minimum or last

outlev 1 # diagnostic output level
trjfrq 1 # trajectory frequency
trjout test.trj # trajectory file
trjsel E # A=acc only;E=either acc or r

I also tried several values for trjbeg and trjend , but in every case I 
got an output with only the values for the first cycle of every run like 
this:

ntorsions 0
run 1
cycle 1
temp 1000.000000
state 1 R 131808.296875 0.000000 45.497338 64.274652 30.326107 -0.668758 
-0.623915 -0.404342 86.532517
state 2 e 1000.000000 1000.000000 47.229206 62.321471 32.220805 
-0.668758 -0.623915 -0.404342 86.532517
&&&
state 304 R 186972.781250 0.000000 47.336364 65.528870 34.041372 
-0.668758 -0.623915 -0.404342 86.532517

ntorsions 0
run 2
cycle 1
temp 1000.000000
state 1 e 1000.000000 1000.000000 59.229028 58.824385 45.100996 
-0.248347 0.186834 0.950482 240.451190
&&&..
..............

Why can't I get the whole Trajectory output?
t it possible to get the coordinates for the states of the other 49 
cycles of every run?

Thanks in advance for your help.

Stephan Tatzel



> ATTACHMENT part 2 application/x-zip-compressed name=main.zip
________________________________________________
--- ADL: AutoDock List --- http://www.scripps.edu/pub/olson-web/doc/autodock/ ---

B.Nataraj,
M.Tech.(Bioinformatics),
SASTRA Deemed University,
(www.sastra.edu)
Thanjavur,
Tamil Nadu,
India.
Email:nataraj at biotech2.sastra.edu
Email:natarajmtech at yahoo.co.uk
		
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