[gmx-users] hydrogen bonding within a peptide

[Kia.Balali-Mood@ed.ac.uk]

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. 

Any ideas will be gratefully acknowledged! 

best wishes to u all

Kia

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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