[gmx-users] NOE restriction for MD using protons with the same chemical shift.

[David van der Spoel]

On Fri, 2004-01-16 at 11:22, Santi Esteban Martin wrote:
> hi gromacs users !
> I wonder if it is possible to treat multiple proton signals correctly.
> I mean, using NMR programs like Xeasy, one can use the QB label if HB2
> and HB3 have the same chemical shift.
> In a topology file where I have defined(the molecule is non-protein
> compound) all protons, I do not know how to treat such cases.
> should be treated, similarly. 
> should I use single particule ?

No, you can do the averaging using explicit atoms. It is described in
the manual. You should use the OPLS force field because it has explicit
protons. Also, there is an xplor2gmx.pl script somewhere. Use it at your
own risk though.

> 
> Eg.:
> 1HCH, 2HCH, 3HCH from methyl group (in UPAC notation) should be let us
> say 1QCH and treat them consecuently ?
> 
> Thanks and go on with gormacs symposium !
> 
> 
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> 
> 
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assist. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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