[gmx-users] hydrogen bonding within a peptide

[David]

On Wed, 2004-01-21 at 18:22, Kia.Balali-Mood at ed.ac.uk wrote:
> Dear Users,
> 
> Does anyone know how to obtain h bonding within a peptide, using trajectory files??
> 
> I know that g_hbond (excellent programme by the way!) can calculate h bonds
> between say peptides and lipid/SPC. I also know that PDB viewers (say RASMOL)
> can tell u the  internal h bonds within a peptide ...but it'd be great to know
> the change in internal h bonds within my little peptide (only 15 residues)
> throughout the sim (4ns) as it's attached to a mixed DOPC/DOPG bilayer. 
> 
just select the protein group twice


> Any ideas will be gratefully acknowledged! 
> 
> best wishes to u all
> 
> Kia
> 
> ******************************************************************************
> Kia Balali-Mood
> Laboratory of Membrane Biophysics
> Division of Pre Clinical Veterinary Sciences
> University of Edinburgh
> College of Medicine & Veterinary Medicine
> The Vet School
> Summerhall
> Edinburgh, EH9 1QH
> Tel. +44 (0)131 650 6142
> Fax. +44 (0)131 650 6576
> leaflet.vet.ed.ac.uk
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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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