AMBER Archive (2005)

Subject: Re: AMBER: a bimolecular reaction

From: Yong Duan (duan_at_albert.genomecenter.ucdavis.edu)
Date: Fri Jul 22 2005 - 12:44:23 CDT

The alcohol hydrogen has a van der Waals zero van der Waals radius,
allowing it collapse to the negatively charge carboxylic acid. You
probably need to turn on SHAKE for all atoms (not limited to hydrogens).

yong
*****************
On Tue, 12 Apr 2005, David A. Case wrote:

> 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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