[Dock-fans] Only rescore, energy C6, C12
William Joseph Allen
william.joseph.allen at gmail.com
Thu Feb 28 08:03:11 PST 2013
In order to compute the score of the ligand alone, you will have to choose
"no" for both "orient_ligand" and "flexible_ligand", and "yes" for
"score_molecules". If you choose to use the "continuous_score_primary"
scoring function, then the only input needed are mol2 files of the ligand
and receptor (both with hydrogens and charges added). An example of the
input file needed for that calculation, compatible with DOCK 6.6, is below.
If you want to do a more advanced calculation, consider setting both
"flexible_ligand" and "minimize_ligand" to "yes". This will likely yield a
lower overall energy.
I'm not sure what you mean by your second question. Are C6 and C12
individual atoms in the ligand?
Be sure to change the contents of this input file to match your file names
and locations. Then execute dock by:
$ dock6 -i dock.in -o dock.out
On Thu, Feb 28, 2013 at 2:53 AM, Václav Bazgier <vaclav.bazgier at upol.cz>wrote:
> I would like only rescore natural ligand in some system. Is there any
> way how to do it?
> When I used autodock vina is there command score_only. I have a problem
> with propreties in DOCK 6.6, I dont't know what is correct settings,
> maybe number of orientations or something else?
> And my second question?
> Is there any way how to read from result energy C6 and C12?
> Thank you for answer and for great program for docking
> Dock-fans mailing list
> Dock-fans at docking.org
William Joseph Allen, Ph.D.
Dept. of Applied Mathematics and Statistics
Stony Brook University
-------------- next part --------------
An HTML attachment was scrubbed...
More information about the Dock-fans