AMBER Archive (2002)

Subject: Re: a question about force field in AMBER

From: sychen (yuann_at_bioinfo.ndhu.edu.tw)
Date: Sat Dec 14 2002 - 23:17:59 CST

On Sat, 14 Dec 2002 21:16:25 -0700
jzhou <jzhou_at_sunkay.cs.ualberta.ca> wrote:
> Hi, Mr. S. Y. Chen
> Thank you for your reply. I know that you have bought AMBER. Have you ever
> used the energy minimization function in it? If you did, could you tell me
> what is the input to the function?
Yes, however, energy minimization is often one step in a whole molecule
simulation job. You may refer to AMBER Tutorials, such as 'DNA' chapter,
to get more detail information which could help you.

>I am still curious on how to tell the bond
> and non-bond pairs ( I don't have any basic knowledge in Organic Chemistry and
> ab-initio calculation ). Do you know how AMBER implement it in the case of
> protein? Is it decided from the stucture of amino-acid and secondary structure
> of protein?
> Thanks.
> Jun zhou
If the initial structure is taken from PDB, LEAP (one module in AMBER)
can edit and build the initial model. AMBER has many specific force
field parameters for nucleic acids, proteins, and general organic
molecules....etc., and LEAP will assign automatically what you need,
including bonding information, according to the force field you pick,
before writing out to the parameter and coordinate file used in further calculation.
You might also take a look at the PDB file if there is irregular residue
and do some editing. There are some examples in AMBER Tutorials related
to this.

Good Luck!

sychen