On Sat, Nov 16, 2002, Monica wrote:
>
> 1) While doing DNA-drug minimization using NMR restraints in vacuum in
> presence of conterions ,the sodium ions are forming triangulated structure
> with Phosphate of DNA.
I don't think it's generally recommended any more to do a vacuum simulation
of DNA with counterions (even with the "big" counterions that I assume you
are using). I'd recommend the GB models (with no explicit counterions)
instead, or explicit solvent calculations. But others may have more
relevant experience or answers.
> 2) Secondly I don't want to put group input on DNA while doing
> minimization but removal of group input leads planer rings of DNA -drug
> to be distorted.
>
I can't tell what sort of "group input" you have in mind, no can I tell
how non-planar the bases or drug are. More specific informations is needed.
...dac
--
==================================================================
David A. Case | e-mail: case_at_scripps.edu
Dept. of Molecular Biology, TPC15 | fax: +1-858-784-8896
The Scripps Research Institute | phone: +1-858-784-9768
10550 N. Torrey Pines Rd. | home page:
La Jolla CA 92037 USA | http://www.scripps.edu/case
==================================================================
Received on Sat Nov 16 2002 - 11:45:01 PST
