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

[Patrick Ladam]

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...


bye and thanX



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| Patrick LADAM                   |                               |
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