AMBER Archive (2003)

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

From: Dr. Yong Duan (yduan_at_albert.chem.udel.edu)
Date: Thu Nov 13 2003 - 09:57:41 CST

Check the official INSIGHT II documentation to find out which version of
the force fields they used.

Many (new) users are confused by the variety of AMBER force fields. There
are at least three versions of so-called AMBER force fields that are in
"circulation" outside the AMBER distribution, including AMBER united atom
model, AMBER all-atom model. These two were developed in 80's. There have
been a lot of studies using these force fields. Because computers were a
bit slower then, a typical appliaction of these two force fields was the
so-called in-vaccuo simulation (with distance dielectric, for instance).

Cornel et al (AMBER 94/parm94/parm96 ...). was developed in 90's and has
been extensively tested and refined for both protein and nucleic acid in
solvated environment.

Another force field that is also related to AMBER is the AMBER* force
field which was a derivative of AMBER force field. But this is not
distributed with AMBER package and I do not know how it behaves. I think
this is the one distributed with INSIGHT II. If this is the case, please
check with official INSIGHT II documentation.

yong
************
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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