[Dock-fans] Can I evaluate scores of bounded conformations without changing coordiates?

Terry Lang terry at cgl.ucsf.edu
Wed Jul 20 09:10:38 PDT 2005

Dear Juyong,

First, to rescore just your starting structure, say no to the orienting
and minimizing and yes to scoring. This set of parameters will allow you
to score the crystal ligand-protein interaction without sampling.
Second, there are a number of things you need to check before jumping to
the conclusion that you have found a bug. 1) Have you installed all of
the bug fixes that we have posted at
http://dock.compbio.ucsf.edu/DOCK_5/index.htm? There are currently
several which apply to the anchor and grow algorithm that may help your
situation. 2) What is the interaction energy between the target and the
ligand you used to parameterize your input file? If it it greater than
-10 DOCK units, you need to reevaluate how you have prepared your system
as DOCK most likely will not be able to recreate such a bad structure.
For the input parameters, our currently recommended parameters are the
default settings during interactive input file generation. We would
STRONGLY recommend against deviating from those parameters by more than
an order of magnitude. The fact that you need so many orientations
suggests that something else is wrong. In answer to your questions, when
we are generating parameters to start with, we generally try to recreate
an experimentally determined orientation within 2 Ang RMSD. The
parameters we have as defaults work relatively well over a range of
systems. It may be possible to create improvement by tweaking these
parameters for your specific system, but once again, you should not need
to tweak them by more than an order of magnitude. You should be able to
DOCK ligands with 10 rotatable bonds.
Finally, if you have tried all of the above and still think you have a
problem, let me know. We do not expect you to debug the code if there is
a problem, but I will need a) more information on exactly where you
think the calculation is going wrong, b) you input files so I can
recreate the problem here, and c) your operating system.

Good luck,

이주용 wrote:

> Hello dock-fans!
> I told you yesterday that I got very strange energy scores from my virtual
> ligand and protein.
> So, I want to test if it is some kind of bug while calculating the
> scores. I think it would be helpful to just evaluate the score without
> changing coorinates of ligand and protein. I tried to do it myself but
> I'm not familiar with C++ so I couldn't fully understand your codes.
> :-(
> I'm wondering that whether I can do it by setting some parameters.
> I'll be very pleased with your kind responses!
> ==================================================
> Graduate student in Seoul National University, Korea
> Computaional biology Laboratory
> Lee, juyong
> drfaust23 at gmail.com <mailto:drfaust23 at gmail.com> // nicole23 at naver.com
> <mailto:nicole23 at naver.com>
> 이주용 Lee, juyong
> Graduate Student - Lab of Computational biology
> Department of Chemistry, Seoul National University, Seoul, Korea.
> <mailto:nicole23 at naver.com>
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>Dock-fans at docking.org

P. Therese Lang
Kuntz and James Labs
UCSF--Chemistry and Chemical Biology
Phone: (415)476-3986


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