rotatable bonds question, using autodock
- From: Susan Heffron <sheffron %-% at %-% uci.edu>
- Organization: University of California, Irvine
- Subject: rotatable bonds question, using autodock
- Date: Mon, 13 May 2002 13:25:50 -0700
Hi.
Forgive my basic chemistry questions... I am planning to dock various
small molecules to a protein using Autodock. Some of my small molecules
have structures such that I am not sure how to assign certain bonds...
rotatable or not (e.g., partial double-bond character or not).
Specifically, my questions are:
1. In a structure with -N-C-N- would there be partial double-bond
"
O
character to both C-N bonds, or only one (like a peptide bond)?
2. In a structure with -N-C-N- would there be a partial double-bond
"
S
character to the N-C and C=S bonds, or not?
Thanks in advance for your help.
Susan
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Susan Heffron
Dept. of Physiology and Biophysics
University of California, Irvine
Irvine, CA 92697-4560 U.S.A.
phone: (949) 824-4625
FAX: (949) 824-8540
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