[gmx-users] intermolecular distance restraints (fwd)

[David van der Spoel]

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
chains.


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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