Dear AMBER users community:
When I tried to minimize the energy of DNA with 24 base pairs using
NMODE, I got " dppsv returns error code: 29" . Anyone has
ideas about it?
Plus, I have a question about the "addions routine" in Leap. The
addions routine calculates the Coulombic potential grid and puts the
sodium ions (Na+) at the points of the lowest eletrostatic potential.
After the first Na+ is set down, the electrostactic potential has to be
recalculated to put the second sodium ion. However, adding the second
ion into the system will change the electrostatic potential again. So
the position of the first sodium ion has to be adjusted according to the
changed potential. Generally, the positions of (N-1) sodium ions have
to be adjusted after the Nth Na+ is added. But I am not clear how "
addions routine" works ? Could anyone give me any ideas or literature
about it?
Thank you very much in advance.
Best,
Xiaowei
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Received on Fri Feb 04 2005 - 18:53:00 PST
