AMBER Archive (2007)

Subject: AMBER: problem related to visualizing of structure

From: deepti nayar (deepti.icgeb_at_gmail.com)
Date: Tue Apr 10 2007 - 01:33:40 CDT

hi

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
dehydrophenylalanine)

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

thanks
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