AMBER Archive (2003)

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

From: Balvinder Singh (bvs_at_imtech.res.in)
Date: Thu Nov 13 2003 - 11:21:49 CST

Most of the querries raised by you are related to InsightII and
can be answered well by Accelrys Inc., if you are still a license holder
with them.
In InsightII2000, it is still the old AMBER version - may be
4.0 or 5.0. - confirm with accelrys
In InsightII, analysis module can help you to analyze the energies of
structural variants.

-Balvinder

On Thu, 13 Nov 2003, a b wrote:

>
> 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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