[MMTK] Naive MC/docking query

hinsen at llb.saclay.cea.fr hinsen at llb.saclay.cea.fr
Thu Dec 9 11:41:23 CET 2004


On Dec 8, 2004, at 18:58, david.evans at ulsop.ac.uk wrote:

> I would like to build a rough-and-ready MC program to dock long,
> flexible ligands into the minor groove of DNA. This would involve
> torsional moves in the ligand, and probably in the nucleic acid as
> well. The intention would be to use this to generate initial guess
> structures before moving into an MD simulation, either in MMTK or
> another program.
>
> I have never used MMTK (don't hit me) but skimmed the MMTK
> documentation and mailing list, and it is not clear to me how much of
> the necessary functionality is built into the program already. I'm

There is all the boring basics (file I/O, energy and force evaluation) 
and a lot of utility routines for manipulating molecules. You would 
have to add the rules for modifying conformations (expressing it in 
terms of operations such as "rotate these atoms around that axis by x 
degrees") and the MC algorithm.

Unless you need unusual force field terms, you can code all of your 
project in Python, no need to go to the C level.

> obviously prepared to do a fair bit of coding myself to get this
> working, but I would appreciate any suggestions about whether MMTK is
> a good place to start for this.

It was designed to make such projects easy, so I hope it will actually 
prove to be a good starting point for you!

Konrad.
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Konrad Hinsen
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