[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

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.


francesco pietra

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