Justin<br><br>I have one extra question about parametrisation of the bond type<br><br>Initially I had -c-c- bond so both atoms were in the sp3 hybridization. I've changed bond type between that atoms to the gb_16 ( from phe ring) to define them as the >c=c< but during the simulation I've noticed that the bond between that atoms is not planar ( sp2 form) and still is in the sp3. What addition changees should I do in my topology to change the planarity of new bond ? <br>
<br><br>Should I make some changes ia angles term as well?<br><br>E.g I've found<br><br> 612 613 614 2 ga_13 ; <br><br>where 612 and 613 are the atoms wich I would like to present as the rigid. I've change to the ga_27 ( 120) but during simulation the bond was still in sp3. What I've done wrong ?<br>
<br>James<br><br><div class="gmail_quote">2012/6/8 James Starlight <span dir="ltr"><<a href="mailto:jmsstarlight@gmail.com" target="_blank">jmsstarlight@gmail.com</a>></span><br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Justin,<br><br><br><br>thanks alot. I'll try to use gb_10 ( for C=N) as well as gb_16 ( for C=C) for parametrisation in my task.<div class="HOEnZb"><div class="h5"><br><br><br>James<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><br>
<br>
On 6/8/12 2:01 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">
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<br>
linnear sequence -C=C-.<br>
<br>
2) is the >C=N- double bond where both atoms in the 5-m ring system<br>
<br>
</blockquote>
<br></div>
This is a better description. The last message suggested everything was in a 5-membered ring. Had that been the case, my suggestion would have been right (see, for instance, a HIS side chain - gb_10 is used for both C=C and C=N in that case).<br>
<br>
There are no linear C=C bonds in Gromos force fields by default, as such groups are not in proteins. The closest you can likely come is to take a C=C bond from the PHE ring. Bond lengths are simple, and are usually derived from spectroscopic information. If using constraints on all bonds, the force constant is irrelevant since the bond is rigid. If not using constraints, then you'll have to find or derive suitable parameters yourself. Welcome to the inconvenient world of parameterization :)<br>
<br>
-Justin<br>
<br>
<blockquote class="gmail_quote" style="margin:0pt 0pt 0pt 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
Thanks again,<br>
<br>
James<br>
<br>
<br>
<br>
2012/6/8 Justin A. Lemkul <<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a> <mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>>><div><br>
<br>
<br>
<br>
On 6/8/12 1:22 PM, James Starlight wrote:<br>
<br>
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<br>
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>
<br>
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<br>
<br>
-Justin<br>
<br>
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