Speaking of rdparm, I don't quite understand the Lennard-Jones output which
looks like this:
Lennard-Jones
Types A C
c1 c1 819971.66 531.10
c1 o 574393.46 555.67
c1 OW 696790.71 564.50
c1 HW 0.00 0.00
OW OW 581935.56 594.83
H OW HW 0.00 0.00
HW HW 0.00 0.00
What does A and C stand for and what are these numbers?
Dian
On Tue, Mar 2, 2010 at 10:40 PM, Jason Swails <jason.swails.gmail.com>wrote:
> 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 - 10:30:05 PST
