[MMTK] Naive MC/docking query

david.evans at ulsop.ac.uk david.evans at ulsop.ac.uk
Wed Dec 8 18:58:48 CET 2004


Dear list,

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
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.

Thank you

Dave Evans
----

School of Pharmacy
University of London



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