Thank you Jason, the world is becoming much more clear. :)
After I have parameterized my molecules (in my case, all 20 residues,
benzene, and a couple of other fairly normal molecules) using Antechamber,
the atom types output in the mol2 file will be GAFF atom types along with
their partial charges, correct? In this case, to get the vdw radii of these
atoms, should I look in the gaff.dat file in the parms directory? When I do
this I see this:
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
h3 1.1870 0.0157 Veenstra et al JCC,8,(1992),963
h4 1.4090 0.0150 Spellmeyer, one electrowithdr.
neighbor
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
hp 0.6000 0.0157 same to hs (be careful !)
hs 0.6000 0.0157 W. Cornell CH3SH --> CH3OH FEP
....
....
....
Am I parsing this correctly to read that the h1 atom type has a vdw radii of
1.3870 and a well depth of 0.0157?
Thanks again!
-denny-
-----Original Message-----
From: amber-bounces.ambermd.org [mailto:amber-bounces.ambermd.org] On Behalf
Of Jason Swails
Sent: Tuesday, March 02, 2010 9:40 PM
To: AMBER Mailing List
Subject: Re: [AMBER] Vdw radii params in antechamber
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 Wed Mar 03 2010 - 10:30:03 PST
