AMBER Archive (2008)

Subject: Re: AMBER: to prepare pdb file fro unusual amino acid.

From: FyD (
Date: Wed Sep 24 2008 - 13:36:03 CDT

Quoting priya priya <>:

> I am looking for some way to prepare pdb files for a molecule with
> unusual amino acid, that is not incluede in Xleap of Amber.
> Can anybody suggest me some tool that can be use to draw the molecule.

Usually when you want to develop a new FF library for a central
fragment of an unusual amino acid (AA) you start from the dipeptide

You can use XLEaP to build this dipeptide:


You edit DIPEPTIDE & add graphically the missing atoms/modify the atom
names/atom types etc... You can use ALA as the 'beginning' of your new
AA if your new AA is L; otherwise you will have to fly the chirality
of ALA.

savepdb DIPEPTIDE dipeptide.pdb

regards, Francois

The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" (in the *body* of the email)