[gmx-users] intermolecular distance restraints (fwd)

David van der Spoel spoel at xray.bmc.uu.se
Tue Sep 18 16:39:07 CEST 2001

On Tue, 18 Sep 2001, Luca Monticelli wrote:

>I am trying to run MD simulations on 2 proteins close in space; they have
>different chain identifiers in the pdb file (.gro files do not support
>multiple chains yet, right?). In order to keep the 2 proteins close in
>space during the MD, I would like to use intermolecular distance
>restraints, but I don't know how to do this with gromacs. The old version
>(2.0) used to have big problems with this - the "normal" distance
>restraint file (disre.itp, that we can include in the topology.top) only
>works in the intra-molecular case, apparently, and does not allow distance
>restraints between different protein chains - did anybody fix this?
I don't think so. It is quite tedious indeed to do so in the code for
pdb2gmx. It is not a problem of mdrun, but just of generating the
topology. Similar problem exist when chemical bond exist between protein

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

More information about the gromacs.org_gmx-users mailing list