Hovakim Grabski wrote:
Dear GROMACS users,
I'm a novice user,
I've been trying to find a way to visualize hydrogen bonds with VMD,but
I haven't been successful.
After running a simulation of 13 Hypericin molecules solved in Water, I
loaded the.gro file and then the trajectory file .xtc, after that in the
Create Representation window I changed to CPK and then modified to show
just the Hypericin molecules (not water).Later I created another
representation and changed to HBONDS and in the panel changed to "name
H O",but VMD doesn't show the HBONDS formed between O and H atoms.
Where is my mistake?
Probably the atom names are wrong. This is a VMD question, so you're better off
posting to the VMD mailing list for help on such topics.
-Justin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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