[gmx-users] distance between protons

David van der Spoel spoel at xray.bmc.uu.se
Wed Jan 14 14:49:00 CET 2004

On Wed, 2004-01-14 at 14:35, Nguyen Hoang Phuong wrote:
> Dear All,
> If the united atom ff like GROMOS is used, how can one calculate the
> distances between protons, e.g. between NH of one residue and H of a side chain of another residue of a protein in order
> to compare with results obtained fro NOE data?
> Thanks,

the protonate program will do just that.
you will need an extra tpr file to do the analysis
> Phuong
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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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