Hello,
You can find van der Waals parameters for atoms that have already been
parameterized in parameter files located in $AMBERHOME/dat/leap/parm/
. The one used for ff99SB is parm99.dat. The vdw parameters are found
near the bottom of that file. If one of your "new" atom types is
similar in description to one of the atom types defined in parm99.dat,
I think it's safe to use its corresponding vdw parameters.
The description for the file format of the parm files is found
http://ambermd.org/formats.html#parm.dat . That should tell you what
you're looking at (namely the van der Waals radius and well-depth,
respectively, for a section labeled "RE").
On Wed, Mar 3, 2010 at 12:08 AM, Denny Bromley
<dbromley.u.washington.edu> wrote:
> Hi all,
>
> I apologize if this is a newbie question; I need to get the partial charges
> and vdw radii for newly parameterized atoms. The partial charges are easy
> to find in the mol2 output file, but the vdw radii are harder to find. The
> closest I've gotten is some of the values in the prmtop file, but this seems
> overly complicated (but maybe not- I'm still very much a novice with
I would avoid going to the prmtop file. You'd have to back out the
radius and well-depth parameters from the A and B coefficients. While
the calculation of A and B from the radius and depth are documented,
the above method is probably easier.
In fact, I would, in general, rarely try to glean information from the
prmtop file through a text editor (use rdparm if you need info from a
prmtop).
> Amber). Are they stored someplace else or is this the place where I should
> be looking?
>
> Thanks for the help!
>
> - denny -
Hope this helped,
Jason
--
---------------------------------------
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Tue Mar 02 2010 - 22:00:03 PST
