On 6/10/12 3:06 AM, James Starlight wrote:
Justin
I have one extra question about parametrisation of the bond type
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 ?
Defining appropriate atom types will be necessary here, as well. For a single
bond, the atom types would be -CH2-CH2- while a double bond will necessarily be
-CH=CH-
Also note that with a united atom representation, it's very hard to make such
assertions about hybridization state. There are no hydrogens, so the geometry
of these central carbons is not easily defined.
Should I make some changes ia angles term as well?
E.g I've found
612 613 614 2 ga_13 ;
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 ?
As there are no parameters for linear C=C bonds in the Gromos force fields, you
may have to do some parameterization yourself, particularly for appropriate
dihedrals. One option is to look at how these bonds are treated in lipid force
fields like the Berger parameter set, distributed by Peter Tieleman's group.
There are double bonds defined for lipids like POPC.
-Justin
--
========================================
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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