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

David van der Spoel spoel at xray.bmc.uu.se
Thu Mar 14 18:20:52 CET 2002

On Thu, 14 Mar 2002, Patrick Ladam wrote:

>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.
Is this the case? That actually sound unlikely. 

>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.
One thing you can do in CNS but not in GROMACS is have scripts with
alternating Annealing and minimization etc., although you can do it
externally in a shell script or perl script calling GROMACS programs. 

In general, if the potential functions match, you can run it in GROMACS.
As we discussed before GROMACS is lacking some utilities for handling
distance restraints (X-ray refinement anyone?)

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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