AMBER Archive (2003)

Subject: Re: AMBER: 'ho' vDW parameters

From: Carlos Simmerling (carlos_at_csb.sunysb.edu)
Date: Mon Sep 08 2003 - 15:10:13 CDT

isn't this the hydroxyl hydrogen that has a
vdw radius of zero to be consistent with
TIP3P water?

----- Original Message -----
From: "Junmei Wang" <JWang_at_encysive.com>
To: <amber_at_scripps.edu>
Sent: Monday, September 08, 2003 4:01 PM
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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