[gmx-users] INTRA-molecular disulphide bridges.

[Leonardo Manzoni]

Actually the situation is the following:
I want to run two simulations of the  peptide, one with CYS-CYS 
intramolecular bond, and the other without it.
Using the -ss option of pdb2gmx I always obtain the same topology, and the 
same output in both cases
should I define (or delete) the bond by hand?
thanks


>From: "K.A.Feenstra" <k.a.feenstra at chem.rug.nl>
>To: gmx-users at gromacs.org
>CC: Leonardo Manzoni <leonardomanzoni at hotmail.com>
>Subject: Re: [gmx-users] INTRA-molecular disulphide bridges.
>Date: Mon, 26 Nov 2001 11:36:19 +0100
>
>Leonardo Manzoni wrote:
> >
> > Hi all,
> >
> > I have to simulate a small cyclic peptide with a disulphide bridge in 
>it,
> > formed by two residues belonging to the same chain.
> > It looks like pdb2gmx can form disulphide bridges only between different
> > chains. Is there a way to form the disulphide bridge INTRA-molecularly?
>
>It is exactly the opposite: pdb2gmx can *not* make inter-molecular
>(between different chains) bonds. I would guess something else goes
>wrong.
>
>--
>Groetjes,
>
>Anton
>  _____________ _____________________________________________________
>|             | Anton Feenstra       Dept. of Biophysical Chemistry |
>|  _   _  ___,| K.A.Feenstra at chem.rug.nl    University of Groningen |
>| / \ / \'| | | Tel +31 50 363 4327                    Nijenborgh 4 |
>|(   |   )| | | Fax +31 50 363 4800               9747 AG Groningen |
>| \_/ \_/ | | | http://md.chem.rug.nl/~anton        The Netherlands |
>|             | "Why, how now, Claudio ! Whence Comes this Restraint|
>|_____________|_____________________________________________________|
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