AMBER Archive (2008)

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

From: FyD (fyd_at_q4md-forcefieldtools.org)
Date: Wed Sep 24 2008 - 13:36:03 CDT

Quoting priya priya <priyaanand_27_at_yahoo.co.in>:

> 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
ACE-AA-NME.

You can use XLEaP to build this dipeptide:

DIPEPTIDE = sequence {ACE ALA NME}

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

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