The Molecular Graphics Laboratory Forum

AutoDock, AutoLigand, MGLTools, Vina, PyRx and more.
It is currently Mon Jul 16, 2018 11:55 pm

All times are UTC




Post new topic Reply to topic  [ 3 posts ] 
Author Message
PostPosted: Mon Jun 15, 2015 5:36 pm 
Offline
Micromolar User
Micromolar User
User avatar

Joined: Sat Aug 08, 2009 2:38 pm
Posts: 49
I am running the Ubuntu v-14.04 LTS based BioLinux v-8 in a 64bit Microsoft 7 Professional VM.

I compiled the autodock source code but when I run a test model using the PyRx GUI the values of Ki are missing in the results. The combined configure and make log is attached. PrintEnergies.cc is compiled to PrintEnergies.o which, in tern, is compiled into the autodock4 executable.

I have successfully compiled and run autodock4 (same version) in a native Debian 7.8.0 OS on another computer.

Please advise.

Thanks in return.


Attachments:
autodock_config_make.log [211.36 KiB]
Downloaded 233 times
Top
 Profile  
 
PostPosted: Mon Jun 15, 2015 7:23 pm 
Offline
Picomolar User
Picomolar User
User avatar

Joined: Sun Jun 21, 2009 11:37 pm
Posts: 163
Now you may need to set a higher level of output in your dpf file in order to output the Ki values:
Currently in autodock4.2 and later, the amount of output in the docking log can be set in the dpf using these symbolic or numeric values for the 'outlev' parameter:

Numeric Symbolic Result
-2 min minimal-energy breakdown and state of one result
-1 minclust energy breakdown, states, coords of clustering results
0 basic echoes input, parms used, final coords and state from each run
1 adt ADT-compatible output during docking
1 default default value is same as "adt"
2 runv more verbose run - expanded output during docking
3 ligread expanded output during ligand setup (e.g., the nonbond matrix)
4 recread expanded output during receptor map setup
5 runvv still more verbose run (e.g., min/max/median per "N" evals)
6 runvvv most verbose supported run (e.g., state vars per "N" evals)
7 etables energy table / scoring function atom-by-atom details
8 nbinte report of nonbond internal energy table (see analysis.cc)
9 nbintev detailed report of nonbond internal energy table (see analysis.cc)

#this information is from autodock/USERGUIDES/AutoDock4.1_UserGuide.pdf (last modified 11/05/2012)...
Alternatively it may be some other compatibility issue between the newer AutoDock output and the PyRx GUI


Top
 Profile  
 
PostPosted: Tue Jun 16, 2015 7:52 pm 
Offline
Micromolar User
Micromolar User
User avatar

Joined: Sat Aug 08, 2009 2:38 pm
Posts: 49
Thank you for the prompt reply. I'll take a ookk at teh settings in PyRx

I just ran the test case in adt and got the Ki values with the default values for the run.


Top
 Profile  
 
Display posts from previous:  Sort by  
Post new topic Reply to topic  [ 3 posts ] 

All times are UTC


Who is online

Users browsing this forum: No registered users and 4 guests


You cannot post new topics in this forum
You cannot reply to topics in this forum
You cannot edit your posts in this forum
You cannot delete your posts in this forum
You cannot post attachments in this forum

Search for:
Jump to:  
cron
POWERED_BY
Translated by MaĆ«l Soucaze © 2009 phpBB.fr