ADL: Vina questions: COM or Center, Search Space, Screening, and Source code
trott at scripps.edu
Fri Jun 12 10:31:42 PDT 2009
On Thu, Jun 11, 2009 at 11:28 AM, Qadri, Yawar<yqadri at physiology.uab.edu> wrote:
> I was playing with Vina and I had a few questions:
> 1. Am I inputting the geometric center or the center of mass of the receptor? I assume you mean the geometric center, but I keep reading COM, so I'd like to be sure.
> 2. For the size of the search space, should I account for the ligand size or is that irrelevant in the search algorithm? For larger ligands, is it necessary to add some buffer space? Is this equivalent to the grid size in AD?
> 3. When virtual screening, it seems that I'm wasting computational cycles recalculating things for each receptor/ligand pair when I assume some stuff could be maintained across the searches. I'm not sure though because the output isn't very verbose.
> 4. Will you be providing the source code? I'd like to look at the code and compile a 64-bit version.
You don't need to manually specify the center of mass or any other
center of the receptor. Vina could have calculated it without the
users' help if it need it.
I suggest watching the tutorial and reading the manual (again, if necessary).
Oleg Trott, Ph.D. (Columbia University)
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