[gmx-users] intermolecular distance restraints (fwd)

Peter Tieleman tieleman at ucalgary.ca
Tue Sep 18 17:32:16 CEST 2001

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.


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

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