AMBER Archive (2003)

Subject: RE: leap complains!

From: Kristina Furse (kristina.e.furse_at_vanderbilt.edu)
Date: Thu May 22 2003 - 18:17:16 CDT

You need an input line like the following in LEaP to add a new atom type:

addAtomTypes {{ "O3" "O" "sp3" }}

Hard to tell if you've done this from your message.

G'luck!

Kristina

>===== Original Message From Layi Adekoya <adekoya_at_fagmed.uit.no> =====
>Hello,
>I need help!!
>I am trying to modell an unnatural amino acid.
>A charged serine (that has lost it's hydrogen)
>I have built it with leap. I have an unstandard
>residue type. I have specified the new type as '03'.since the oxygen
>ceases to be the usual hydroxyl oxygen.
>Leap is however complaining saying the new type not found.
>What do I do to help leap accept this new type?
>I am using amber7.
>
>Help will be greatly appreciated.
>
>Layi

****************************************************
Kristina E. Furse
Department of Chemistry
Center for Structural Biology
Vanderbilt University
email: kfurse_at_structbio.vanderbilt.edu