AMBER Archive (2006)

Subject: Re: AMBER: Atoms overlapping

From: Nitin Bhardwaj (nbhardwaj_at_gmail.com)
Date: Mon Dec 11 2006 - 14:48:53 CST

thanks Dac,
   That makes sense why H1 would overlap with O2. I was thinking if I can
change *JUST* the vDW parameters for 'ho' to some similar H atom (say 'hn')
in gaff.dat after making a separate copy of this dat file. How advisable is
that? Will I have to change any other parameters? I have a feeling that I
will have to adjust some other parameters too.

I can not use SHAKE, as I am not running this simulation in Amber, but in
NAMD. I create the system files (prmtop and inpcrd) in amber. I can not
specifically SHAKE one particular bond if I am using NAMD to run it.

Also, which of these two columns is the vdW radius? There are two values
equal to 0 for 'ho'.

MOD4 RE
  h1 1.3870 0.0157 Veenstra et al JCC,8,(1992),963
  h2 1.2870 0.0157 Veenstra et al JCC,8,(1992),963
  h5 1.3590 0.0150 Spellmeyer, two electrowithdr.
neighbor
  ha 1.4590 0.0150 Spellmeyer
  hc 1.4870 0.0157 OPLS
  hn 0.6000 0.0157 !Ferguson base pair geom.
  ho 0.0000 0.0000 OPLS Jorgensen,
JACS,110,(1988),1657

thanks a lot,

Rgds,
Nitin

On 11/12/06, David A. Case <case_at_scripps.edu> wrote:
>
> On Mon, Dec 11, 2006, Nitin Bhardwaj wrote:
>
> > I am having a strange problem during my simultion. For one of my
> lipids, I
> > have a hydrogen (say H1) connected to an Oxygen (say O1). O1 is in turn
> > connected to Phosphorus (P). Also connected to P is another oxygen (say
> O2)
> > that is negatively charged. Picture is sthg like this:
> >
> > O2-----P----O1---H1
> > |
> > |
> > C
> > Now if I use amber atomtype (instead of gaff), in the first step of
> > minimization itself, H1 almost overlaps with O2 (distance being 0.001Ang)
> > while still being bonded to O1. I checked the parameters:
> >
> > H1 is atomtype 'ho' (charge 0.4233), O1 is 'oh' (charge -0.7908) and O2
> is
> > 'o' (charge -0.8586).
>
> This is a common problem with phosphates and similar types of structure
> (such
> as yours). Basically, the ho atom type (which is gaff, not amber) has
> zero
> van der Waals parameters, which allows it potentially to overlap with
> negatively charged atoms (such as O2). For water and hydroxides, this can
> be prevented by shaking the O1-H1 bond, (because then the repulsion with
> the
> O1 vdW shell prevents fusion). But this does not seem to be sufficient
> for
> the sort of geometry you have above.
>
> In my view, this is a deficiency in the gaff (and Amber)
> parameterizations.
> Junmei may have some comments here. One workaround we have used is
> illustrated in the "modified tRNA" parameters you can find at the
> contributed
> parameters data base (off the Amber web site): we added an artificial P-H1
> bond, effectively keeping the P-O1-H1 unit fixed (via shake, somewhat like
> a
> water molecule). This "works" in the sense that it prevents the bad
> overlaps
> (or did for us), but we never extensively tested the realism of the
> resulting
> configurations. But maybe something like this would work for you.
>
>
> >
> > Also, the charges written in the prmtop file for all these atoms are
> > different (they are, respectively,
> > 7.71386404E+00 -1.44094659E+01 -1.56451201E+01).
>
> Charges in the prmtop file are the "real" charges multiplied by 18.2223.
> See http://amber.scripps.edu/formats.html#topology.
>
> ...dac
>
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