AMBER Archive (2006)

Subject: AMBER: ff for drug-dna complex and drug atom types assignment

From: Kateryna Miroshnychenko (kateryna_mirosh_at_ire.kharkov.ua)
Date: Mon Oct 23 2006 - 11:08:59 CDT

Dear all,

I want to simulate DNA-drug complex, but after reading mail archive I'm
still unsure what will be the best choice for the force field: I'm
hesitating between ff98 and ff99 or may be mix of them (98 for DNA, 99 for
drug). As it is written in the manual, ff98 is tuned for nucleic acids
whereas ff99 is better for organic molecules. What will be your
advice?

Besides I have question about the assigning atom types for the carbon
atoms in the chromophore of the drug (see attached figure). Should
they all (except that in C=O group) have CM or CA type?

Thank you in advance,
Katya
  

********************************************
 Kateryna Miroshnychenko
post-graduate student
Department of Biological Physics,
Institute of Radiophysics and Electronics,
National Academy of Sciences of Ukraine,
12, Proskura st., Kharkiv, 61085, Ukraine
E-mail:kateryna_mirosh_at_ire.kharkov.ua
********************************************

chromophore.jpg

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