[gmx-users] intermolecular distance restraints (fwd)

[Peter Tieleman]

You could perhaps use the umbrella sampling options (pull stuff) in 
mdrun to restrain the two chains, by defining two groups in an index 
file (maybe the two chains, or a subset of them) and chosing an 
appropriate force constant for the harmonic umbrella potential? You'd 
just need a normal topology for the system, without the restraints, but 
you can only have 1 restraint at the moment.

Or maybe a better solution is to just treat the protein as 1 molecule in 
pdb2gmx, that just happens to miss some bonds/angles/dihedrals that link 
the two halves of the molecule. Depending on your termini, it might take 
a bit of work to get that right, but I've seen it done before.

Cheers,
Peter

David van der Spoel wrote:

> 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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-- 
Dr. D.P. Tieleman
Assistant Professor, AHFMR Scholar
Department of Biological Sciences, University of Calgary
2500 University Drive NW, Calgary, Alberta, Canada T2N 1N4
web: www.ucalgary.ca/~tieleman  fax: (403)289-9311 phone: (403)220-2966