AMBER Archive (2007)

Subject: Re: AMBER: Basic AMBER question

From: Melinda Layten (mlayten_at_gmail.com)
Date: Wed Jul 11 2007 - 15:05:11 CDT

Look at the tutorial B4.
*Using Antechamber to Create Leap Input Files for Simulating Sustiva
using the General Amber Force Field*

>From the tutorial menu off the Amber home page.
http://amber.scripps.edu/tutorials/

On 7/11/07, Lili Peng <lilipeng_at_gmail.com> wrote:
>
> Dear AMBER users,
>
> This is probably a very basic question addressing the fundamentals of
> AMBER.
>
> Currently I've drawn a structure consisting of an amino acid chain and
> organic molecules (consisting of benzene rings and a carbohydrate). I used
> Accelrys' DS Visualizer to draw the structure in .PDB format. Now I'm
> attempting to perform an energy minimization in AMBER, but I'm getting
> errors such as "FATAL: Atom .R<MOL 2>.A<C104 23> does not have a type." I
> Googled this error and I found some infromation about incorporating .lib
> files. I figured this has to do with the different types molecules in my
> structure - or does it?
>
> Basically, I'd like to know if AMBER can be used to simulate a complex
> structure consisting of different types of molecules? I've read that AMBER
> is primarily used for simulation on proteins and DNA, but what if I wanted
> to do simulate organic molecules? I've read into other literature, and from
> what I've gathered there are other force fields such as ECEPP and Compass
> that are better suited for organic molecules.
>
> Anyway, I'm probably asking a very basic question, but I'd like to whether
> I need to back up a few steps before I proceed further with using AMBER.
>
> Thanks all,
> Lili
>

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