AMBER Archive (2005)

Subject: Re: AMBER: Disulfide bond

From: FyD (fyd_at_u-picardie.fr)
Date: Fri Apr 08 2005 - 11:09:03 CDT

Quoting michael chen <michael_chen1_2000_at_yahoo.com>:

> I am wondering generally how to incorporate a
> disulfide bond in the all-atom simulation.
> Does people simulate a disulfide bond as covalent-bond
> or sth.? Does anybody happen to know some literature?
> If as a covalent-bond, how to define it in amber
> preparation?

- In AMBER, cystine are CYX and not CYS. You have to rename them in your PDB
file...
- In LEaP, you also have to make the SS bond...
See the 'bond' command in AMBER8/LEaP doc. page 53. 

-- 
  F.-Y. Dupradeau
DMAG EA 3901 & Faculte de Pharmacie, Amiens, France
The Scripps Research Institute, La Jolla, CA, USA
       --
http://www.u-picardie.fr/labo/lbpd/FyD.htm
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