Justin,<br><br>Does the gb_10 suitable for both bonds that I want to parametrise ?<br><br>As I've told previously I need to parametrise two different bonds<br><br>1) is the >C=C< bond wich are not in the ring. This is just double bound in linnear sequence -C=C-.<br>
<br>2) is the >C=N- double bond where both atoms in the 5-m ring system<br><br>Thanks again,<br><br>James<br><br><br><br><div class="gmail_quote">2012/6/8 Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>></span><br>
<blockquote class="gmail_quote" style="margin:0pt 0pt 0pt 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div class="im"><br>
<br>
On 6/8/12 1:22 PM, James Starlight wrote:<br>
<blockquote class="gmail_quote" style="margin:0pt 0pt 0pt 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
I've found that information in ffbonded.itp but I'm not sure about exactly<br>
meaning of some types.<br>
<br>
<br>
E.g I'm looking for bond type for simple double bond between C=C as well as C=N<br>
( here both atoms in 5-m ring) atoms pairs. Should I use for the first one<br>
#define gb_15 0.1390 8.6600e+06<br>
; CH2 - C, CR1 (6-ring) 800<br>
<br>
and for the second one ;<br>
<br>
#define gb_11 0.1340 1.0500e+07<br>
; C - N, NZ, NE 900<br>
?<br>
<br>
</blockquote>
<br></div>
Neither. gb_10 sounds exactly like what you need:<br>
<br>
#define gb_10 0.1330 1.1800e+07<br>
; C, CR1 - N, NR, CR1, C (peptide, 5-ring) 1000<span class="HOEnZb"><font color="#888888"><br>
<br>
-Justin<br>
<br>
-- <br>
==============================<u></u>==========<br>
<br>
Justin A. Lemkul, Ph.D.<br>
Research Scientist<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.<u></u>vt.edu/Pages/Personal/justin</a><br>
<br>
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