[Dock-fans] Unbiased docking

Francesco Pietra chiendarret at yahoo.com
Fri Sep 28 10:33:24 PDT 2007


Although not yet ready with DOCK6.1 installation, inspection of tutorials
prompts a couple of questions that may help planning.

What I want to do at the moment is verifying if there is docking at all between
a family of natural products and a complicated protein. Not in a bilayer for
the moment.

I have already carried out a conformational search for my natural products by
simulated annealing with an algorithm that calls Amber9. Parameter and
coordinate files for Amber9 were built with Antechamber/Divcon (ie AM1).

The tutorial on DOCK web site starts from a protein-ligand complex, ie from a
definite receptor site in the protein. Is any graphical or alphanumeric
tutorial for the unbiased docking I am aimed at?

DOCK6.1 is being compiled on a parallel amd64 machine (Debian Linux amd64 with
4GB RAM per cpu, ie a machine better suited for ab initio calculations than
classical MD), where also Amber9 is installed. Although the X system exists (in
fact, xleap requires it) and even Gnome could be called, the machine is
normally used with X killed. I manage anything graphical for Amber9 (to the
exception of xleap) on a single-Athlon desktop (Debian Linux i386 etch). The
two machines are scp linked, which is the way I exchange files between the two
machines.

At 32bit I (1) prepare pdb files for "small molecules" with a MM package; (2)
examine everything graphical with VMD.

On these basis, where to install Chimera for DOCK? I noticed that Chimera calls
both Dock Prep and Antechamber.

Similarly, where to install dms for DOCK?

I understand that these are generic question, normally not for mailing lists.
Though, a couple of suggestions would greatly help me (an organic chemist, just
now beginning to touch the area of the biochemist) in the high complexity of
the docking affairs.

Thanks

francesco pietra


       
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