how to turn off self repulsion

From: Marcela Madrid <>
Date: Tue 21 Nov 2000 14:39:45 -0500


Does anybody know how to turn off electrostatic self repulsion in amber?
I am calculating the free energy difference of a neutral and charged DNA base
using GIBBS. The problem is that for the charged one I am adding
some charge to each heavy atom of the base, and these charges are not
suppose to interact with each other.
How are self repulsions turned off in gral, like for bonded atoms? Is there
only one exclusion list?
thanks, Marcela
Received on Tue Nov 21 2000 - 11:39:45 PST
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