[gmx-users] INTRA-molecular disulphide bridges.

David van der Spoel spoel at xray.bmc.uu.se
Mon Nov 26 17:28:44 CET 2001

On Mon, 26 Nov 2001, K.A.Feenstra wrote:

>Leonardo Manzoni wrote:
>> 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?
If I understand it correctly it is the usual problem... pdb2gmx will only
search for cys-cys bonds in a molecule. The intra-molecular is thus not a
problem (and you can do that manually using the -inter flag or so) but the
intermolecular SS bridge is a problem. I don't know of a workaround.

Groeten, David.
Dr. David van der Spoel, 	Biomedical center, Dept. of Biochemistry
Husargatan 3, Box 576,  	75123 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://zorn.bmc.uu.se/~spoel

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