[gmx-users] Dihedrals in a Sugar Ring???(was atom type not found)

[David]

On Tue, 2002-07-09 at 02:33, Patrick Ladam wrote:
> Hi again,
> 
> Well I am on my way of adding missing bonds and angles in my .itp file for an
> all-hydrogen
> version of ff_gmx2 (I want to drop AMBER parameters in there later on).
> Concerning bonds and angles, grompp asks me to give values and constants for my
> newly
> included hydrogen atoms. That's OK and I add them with no problem.
> 
> Now I am at the point where I have to parametrize dihedrals, I expected grompp
> to ask me
> about dihedrals concerning my 'fresh' hydrogens but to my surprise I also have
> to parametrize
> dihedrals for previously existing heavy atoms like:
> 
> O5'-C5'-C4'-O4'
> C5'-C4'-C3'-C2'
> O4'-C1'-C2'-C3'
> and so on
> 
> How come these dihedrals are not already parametrized (conformational
> equilibrium in
> the pseudo-rotation circle is crucial in Nuc. Acids, it is different in A and B
> DNA for instance).
> Is it taken into account by valence angles ??? Is there a different way to
> handle dihedrals
> in a ring...? If someone can help...
In principle dihedrals are part of the parametrization, and if you
modify the potential by adding hydrogens you have to change them too.
This is not trivial, but for ring systems the number of conformations is
limited. Basically you have to get the relative free energies and the
barriers correct. Maybe you can construct the different conformers of an
isolated ring, and compute their energy (using one step MD). Ideally you
want to compare to Ab Initio calculations.

> 
> 
> bye and thanX
> 
> 
> 
> --
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-- 
Groeten, David.
________________________________________________________________________
Dr. David van der Spoel, 	Biomedical center, Dept. of Biochemistry
Husargatan 3, Box 576,  	75123 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://zorn.bmc.uu.se/~spoel
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