AMBER Archive (2005)

Subject: Re: AMBER: MD problems/shake-many thanks

From: blakrose_at_gazeta.pl
Date: Tue Dec 20 2005 - 17:04:24 CST

Dear Professor Cheatham!

Thank you for helping me.
The calculations are good now, and everything is right.
Many many thanks once again!

Pawel Gruszczynski
University of Gdansk
Chemistry Department

> Yes, this is a ligand (ATP) problem. The atoms HO-OH in the first
> phosphoreus group. The parameters to ATP are from parm94.dat.
> I have tried to do dynamics on isolated ligand having shake on,
> and that is a problem. I got the SHAKE error again on the same
> atoms:
> "Coordinate resetting (SHAKE) cannot be accomplished,
> deviation is too large
> NITER, NIT, LL, I and J are : 0 0 1 1 2

As a followup to the list regarding what was happening and what to
look
for... If you have an isolated ligand and SHAKE failures are
evident in
MD simulation, something is likely funny with the parameters that
allows
atoms to move within vdw spheres leading to large forces such that
the
integrator or SHAKE fails. Working with Pawel, I obtained the
prmtop/inpcrd and did some experimenting.

(1) If you get SHAKE failures on your drug/ligand, try first
extensive
minimization of the isolated compound in-vacuo. If atoms are
penetrating
vdw spheres (leading to overlap), this will be readily apparent
when
looking at the structure. In this case, the HO atom (with no vdw
parameters) overlapped with a nearby oxygen. This is occurring
since the
HO atom has a relatively large (~ +0.4) charge and strongly
interacts
favorably with the nearby oxygens (~ -0.6 charge). As there is no
vdw
repulsion, this attraction overcomes the bond and angle forces
holding
it away.

(2) Running MD simulation on the isolated system in-vacuo shows
that
temperature cannot be maintained (it quickly rises) which is
further
evidence of the instability.

I got around this problem (assuming the charges were reasonable) by
adding a vdw potential to this hydrogen. I changed the OH
parameters
(for this compound) to have a small vdw like HS (0.6 0.0157) and
then
minimization and MD were stable (although the hydrogen in question
is
still very strongly attracted to the nearby oxygen, it does not
penetrate
the vdw sphere).

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