Hello Dong-- > I'm now refining a G-quadruplex structure using a modified refine.py > based on the script in dir egiput/dna_refi of xplor-NIH. The input data > is only noe constraints. > > My question is if I use Lennard-Jones and electrostatics and add the lines > in refine.py:
It's almost certainly a bad idea to turn on electrostatics during structure calculations in the absence of solvent, and perhaps counter-ions, in the case of nucleic acids. For the case of nucleic acids, the ORIE position/orientation database potential has been shown to capture many structural features without the need to employ a full force field. Now, one can *evaluate* and perhaps even do local gradient minimization using L-J and electrostatic potentials. Please contact me if you have further need for using realistic nonbonded energies. > ... > > The output is fine.But the program will give the message: > InternalDynamics::step: large timestep detected. Halving. Occasionally getting these messages is fine, but if you get a whole bunch and the stepsize stays a ridiculously low value (say 1e-8ps) there's clearly a problem. best regards-- Charles
-- Charles Schwieters email: [email protected] www: http://schwieters.org/cds phone: (301) 402-4914 PGP key: http://schwieters.org/cds/pgp.txt
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