On 6/8/12 2:01 PM, James Starlight wrote:
Justin,
Does the gb_10 suitable for both bonds that I want to parametrise ?
As I've told previously I need to parametrise two different bonds
1) is the >C=C< bond wich are not in the ring. This is just double bound in
linnear sequence -C=C-.
2) is the >C=N- double bond where both atoms in the 5-m ring system
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).
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 :)
-Justin
Thanks again,
James
2012/6/8 Justin A. Lemkul <jalem...@vt.edu <mailto:jalem...@vt.edu>>
On 6/8/12 1:22 PM, James Starlight wrote:
I've found that information in ffbonded.itp but I'm not sure about
exactly
meaning of some types.
E.g I'm looking for bond type for simple double bond between C=C as well
as C=N
( here both atoms in 5-m ring) atoms pairs. Should I use for the first
one
#define gb_15 0.1390 8.6600e+06
; CH2 - C, CR1 (6-ring) 800
and for the second one ;
#define gb_11 0.1340 1.0500e+07
; C - N, NZ, NE 900
?
Neither. gb_10 sounds exactly like what you need:
#define gb_10 0.1330 1.1800e+07
; C, CR1 - N, NR, CR1, C (peptide, 5-ring) 1000
-Justin
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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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