VMD-L Mailing List

From: Irene Newhouse (einew_at_hotmail.com)
Date: Mon Mar 30 2009 - 20:39:59 CDT

Thanks very much!

 

Irene
 
> Subject: Re: vmd-l: How to add heme to dowser plugin?
> From: akohlmey_at_cmm.chem.upenn.edu
> To: einew_at_hotmail.com
> CC: vmd-l_at_ks.uiuc.edu
> Date: Mon, 30 Mar 2009 21:24:24 -0400
>
> On Mon, 2009-03-30 at 14:27 -1000, Irene Newhouse wrote:
>
> hello irene,
>
> > Got distracted by other work, and have just gotten back to the
> > question of adding
> > heme to the dowser dictionary & parameters. I got one of the free
> > distributions of gromos, and
> > put that up, & started looking through the ffgmx* files, as
> > recommended on a link
> > from the dowser plugin page. To make sure I had the right thing, I
> > started looking for values
> > identical to those listed for N:
> >
> > This is in dowser:
> >
> > REMARK atomtype LJ-a LJ-b MS-radius
> > TYPE N 49.36 1300.0 2.40 # any Nitorgen
> >
> > While the closest thing I can seem to find is in ffmgxnb.rtp, where
> > the apparently relevant
> > comment line reads:
> >
> > ;name at.num mass charge ptype c6 c12
> > & N reads:
> > N 7 14.00670 0.000 A 0.24362E-02
> > 0.16924E-05
> >
> > Am I looking at the right thing? If so, how do I transmogrify the c6 &
> > c12 values into those
> > in dowser?
>
> well, one of them are espilon/sigma from the more commonly used
> representation of the LJ potential and the second the prefactors
> to the powers of 1/r. best you have a look at, e.g. the gromacs
> manual (i just looked it up, page 50, point 4.1.1 of the version 4.0
> manual) and you see how to convert it. now all you need to find out
> is what unit epsilon is in (note that gromacs uses nanometers as length
> and not angstroms), and whether the epsilon in dowser does contain the
> 4 or not. in most cases it is not, but in some it is.
>
> hope that helps,
> axel.
>
> >
> > Thanks!
> > Irene Newhouse
> >
> >
> >
> > ______________________________________________________________________
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>
> --
> =======================================================================
> Axel Kohlmeyer akohlmey_at_cmm.chem.upenn.edu http://www.cmm.upenn.edu
> Center for Molecular Modeling -- University of Pennsylvania
> Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
> tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425
> =======================================================================
> If you make something idiot-proof, the universe creates a better idiot.
>

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