[gmx-users] conformational study of a dual domain protein

David van der Spoel spoel at xray.bmc.uu.se
Mon Sep 30 10:04:42 CEST 2002

On Mon, 2002-09-30 at 09:43, Bert de Groot wrote:

> it all depends on what kind of restraints you have between the domains.
> If these can be translated into distance restraints (or actually distance
> bounds), then concoord could indeed be used to obtain insight in the
> conformational freedom of the two domains wrt each other.
> the software can be downloaded from:
> http://www.mpibpc.gwdg.de/abteilungen/071/bgroot/concoord.html
> Some manual intervention might be required to include your additional
> interdomain restraints. Let me know if you need help.

There is also a GROMACS version of concoord (cdist/disco), I'm not sure
whether it is good enough for production. It has some features that
Bert's doesn't (tetragonal smoothing, parallel version), but I don't
know whether it produces the same results... Whoever tries to run these
programs, please try Bert's version, which is the authorative version,
as well as the GROMACS version and report back to the list...

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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