AMBER Archive (2003)

Subject: AMBER: RNA and Protein questions (also some general questions)

From: a b (asittner_at_lycos.com)
Date: Thu Nov 13 2003 - 04:55:07 CST

hi, i'm a novice w/ AMBER ,so i have many questions.
if you tou can only answer some of the questions ,it's fine too.

i'm using INSIGHT II AMBER/CHARMM, in order to minimize a mixed RNA/Protein structure (possibly w/ some other small ligands).
1. most of the mass consists of RNA, but the protein interactions w/ the small ligand are the most important.
2. which potential/parameters are recommended in such case? (can you back this up w/ references?)
3. is the answer the same for dynamics?
4. when i select a force field, i only have one AMBER option : "AMBER". do you know what is the default AMBER version for INSIGHT II 2000? how can i get other versions?
5. i would like to compare the energies of structural variants, how do i do that?

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