ADL: Doubt about AutoDock Vina (Redocking)

Oleg Trott trott at scripps.edu
Thu Jan 23 10:47:32 PST 2014


Hi

On Wed, Jan 22, 2014 at 11:26 AM, Renata Parruca da Silva
<renataparruca at yahoo.com.br> wrote:
> Hi, My name is Renata Sakata, I'm PhD student from Unicamp, Brazil. I have a doubt about Redocking.
> How can I get values asRMSD from reference structure (the ligand in the original crystallographic structure),

For aesthetic reasons, Vina doesn't use reference structures as
additional input. You could calculate the RMSDs between structures
with, e.g. Vrms, or other software (You'd need to split the output
first, and convert it to SDF or another appropriate format).

I believe ADT can do this as well, for a somewhat different definition
of "RMSD". Perhaps Ruth will comment on this.

> Population in the optimum cluster (%), Maximum No. of energy evaluation and GA runs to perform a docking validation.

Vina doesn't use genetic algorithms. I'm surprised how many people are
confused about this. You can control the time-vs-exhaustiveness
trade-off using the "exhaustiveness" parameter (see the FAQ and the
video tutorial).

-- 
Oleg Trott, Ph.D. (Columbia University)

Staff Scientist in the Olson Lab
The Scripps Research Institute

http://olegtrott.com


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