AMBER: problem related to visualizing of structure

From: deepti nayar <>
Date: Tue, 10 Apr 2007 12:03:40 +0530


I have made a dipeptide using xleap. my peptide is a non-standard
residue and so i saved the library first and then made the structure.i
have added suitable bonds and atoms as per my requirement. but when i
visualize it using vmd, i could see some unnecessary bondings there. i
was wondering if there is some mistake in the structure that i built
using xleap. its a phenylalanine-dehydrophenylalanine dipeptide.(i
have added the double bond between alpha carbon and beta carbon in

i would be obliged if somebody tells me where is the problem

The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to
Received on Wed Apr 11 2007 - 06:07:34 PDT
Custom Search