[gmx-users] NMR refinement on Nucl. Acids...

Patrick Ladam ladam at smbh.smbh.univ-paris13.fr
Fri Mar 15 01:23:25 CET 2002

Hi all,

I work on NMR structure determination of Nucl. Acids. So I might use the
all-hydrogen forcefield
which is dedidated to this type of work. Unfortunately, this only concerns
Proteins so I have to
build my own Nucl. acids in the ffgmx2 topology file.

At this point I considered importing forcefield parameters from the all-hydrogen
for Nucl. acids in CNS. Well this turns out to be a larger problem than what I
thought at first:

1) It might not be meaningfull to use the CNS equilibrium values and force
constants if the
equation (the potentials) differ.

2) What about the protocols, for instance in CNS, the simulated annealing
are different if you work on a protein or on Nucl. Acids. I once made a mistake
letting default
values for proteins and let me tell you the results were not really satisfying.

So at this point I don't really know what to do, it sounds like a heavy work to
me. What's
your opinion, does anybody have any experience in Nucl. Ac + NMR + Gromaccs?
Do you guys at GMX plan to develop this topic later on?


| Patrick LADAM                   |                               |
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