AMBER Archive (2005)

Subject: Re: AMBER: a bimolecular reaction

From: duan_list_at_albert.genomecenter.ucdavis.edu
Date: Tue Apr 12 2005 - 13:00:14 CDT

This was probably caused by one (or more) atoms that seem to have
charges, yet without van der Waals, at the unperturbed (initial) state.
Note, "HO" also has a zero van der Waals radius and is likely involved in
this "fussion" process. Other possibilities include the dummy atoms, if
you have any. If you only want to let the atom disappear, the atoms should
also have bonds, etc, at the unperturbed state, unless, somehow the bond
(and angle) parameters became zero.

Good luck!

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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