[gmx-users] INTRA-molecular disulphide bridges.
leonardomanzoni at hotmail.com
Mon Nov 26 12:08:10 CET 2001
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?
>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
> > 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
> _____________ _____________________________________________________
>| | 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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