[AMBER] free radicals in amber

From: Ashutosh Shandilya <izerokelvin.gmail.com>
Date: Thu, 27 Jan 2011 13:45:08 +0530

Hi all
I am doing calculation for Fe -O complex where there is a free radical on
one of the oxygen. After making the library file in and adding the required
bond lengths, bond angle and dihedral parameter I was able to make the
topology and coordinate file and did the minimization.
So the question is can I do simulation with free radicals without changing
anything in the force fields aka .gaff file.
Or is there anyway to do that and if I could do that shall I start the
simulation with the same topology and coordinate file.
Any help is highly appreciated.

*Ashutosh Shandilya*
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Received on Thu Jan 27 2011 - 00:30:08 PST
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