On Wed, Apr 06, 2005, Eric Hu wrote:
> Hi, I am experimenting a TI perturbation with Amber 8.0 on an
> enzyme-catalyzed bimolecular reaction (an alcohol reacts with a
> carboxylic acid to form an ester).
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 200 -1.1864E+07 2.6376E+11 2.1022E+12 H15 15
>
> BOND = 6.6603 ANGLE = 78.2334 DIHED = 38.3939
> VDWAALS = -2.9575 EEL = 54.6011 HBOND = 0.0000
> 1-4 VDW = 12.2257 1-4 EEL = ************* RESTRAINT = 0.0000
Take a look visually at the structure after 150 steps or so, and see if you
can figure out which atoms are getting close to each other (leading to a very
large, negative 1-4 EEL term). That might provide some clue, although I don't
know why the 1-4 vdw is not increasing...
....dac
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Received on Tue Apr 12 2005 - 18:53:00 PDT
