AMBER Archive (2003)

Subject: RE: AMBER: 'ho' vDW parameters

From: Yong Duan (yduan_at_udel.edu)
Date: Mon Sep 08 2003 - 15:27:48 CDT

The failure should also vanish if you use SHAKE in minimization. Then,
you will get minimization failure which is acceptable to me (hey, my
standard is pretty low these days).

yong

> -----Original Message-----
> From: owner-amber_at_scripps.edu
> [mailto:owner-amber_at_scripps.edu] On Behalf Of Junmei Wang
> Sent: Monday, September 08, 2003 4:01 PM
> To: amber_at_scripps.edu
> Subject: Re: AMBER: 'ho' vDW parameters
>
>
>
>
>
>
>
> I think the vDW parameters of 'ho' was borrowed from parm94
> force field
> directly. I also found some minimized phosphates and sulfates
> are broken
> using gaff.dat with a dielectric constant of 1 (gas phase) in
> our test of
> the general amber force field (am1-bcc charge). However, if dielectric
> constant of 4 (gas phase) was used, the failure vanished.
> Anyone knows why
> vDW radius of "HO" is set to 0.0 in parm94?
>
> Best
>
>
> Junmei
> ===============================================================
> Dr. Junmei Wang
> Chemistry & Biophysics
> Encysive Pharmaceuticals
> 7000 Fannin, Houston TX 77030
> Tel: 713-5786649
> Email: jwang_at_tbc.com
> Homepage: http://sigyn.compchem.ucsf.edu/members/jmwang/index.html
> ===============================================================
>
>
>
>
>
> "Lee, Matthew"
>
> <mrlee_at_amgen.com>
>
> Sent by:
> To
> owner-amber_at_scrip "'amber_at_scripps.edu'"
>
> ps.edu <amber_at_scripps.edu>
>
>
> cc
>
>
> 09/05/2003 05:33
> Subject
> PM AMBER: 'ho' vDW
> parameters
>
>
>
>
> Please respond to
>
> amber_at_scripps.edu
>
>
>
>
>
>
>
>
>
> I'm curious as to why the 'ho' vDW parameters in gaff.dat
> were set to mimic
> the OPLS hydrogens, with 0.00 vDW radii.
>
> I found, that in neutralized phosphates and sulfates, this can lead to
> disastrous effects, since 1-3 VDW repulsons are ignored in
> AMBER between
> the
> two oh's, instead treated implicitly in the valence angle.
> If an 'ho' is
> bumped close enough to its neighboring 'oh' (not the 'oh' that it is
> covalently bound to), the attraction between 'oh' and 'ho'
> grows infinitely
> large and causes LINMIN failures. This is because the
> oh-p5-oh angle term
> is the only thing to deter this and maxes out at around +45
> kcal/mol as
> does
> the ho-oh-p5, which provides for only 90 kcal/mol of repulsive energy.
> Very
> quickly, the 'oh' and 'ho' can be superimposed on top of one
> another and
> their infinite electrostatic interaction dominates the 90 kcal/mol of
> repulsive angle terms.
>
> ho ho ho
> / / /
> oh oh -----> oh-ho|oh
> \ / | /
> \ / | /
> p5 p5
>
> Since the vDW radius of oh is 1.721 and the bond distance
> between oh-ho is
> 0.96, a vDW radius for 'ho' of 0.6, like all the other h's in
> gaff.dat,
> would still leave the 'ho' within the radius of the 'oh'
> *and* prevent the
> atom superposition.
>
> Is there a reason I missed for why the 'ho' radius should not
> be set to a
> non-zero value?
>
> I read a 1/2003 post by Case on the reflector discussin phosphates in
> nucleic acid simulations, that talked about adding a covalent
> bond between
> the P and the H. I can see that this would also help to
> deter the atom
> superpositions and am wondering if that has any advantages
> over increasing
> the vDW radius of the 'ho' to a non-zero value.
>
> thanks,
> --Matthew
>
>
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