Thanks Jason and Daniel. I am using topotools (A plugin in vmd). You can
load the mol2 file generated by antechamber in vmd.
Then use topotools guessimproper in vmd to get the impropers for the
system. The improper definition it employs is
"Guess improper angles. Are defined for atoms that are bonded to *exactly*
3 atoms when they form a near flat structure. The tolerance flag can be
used as a cutoff for what is to be considered as "flat" and what not. "
You can now compare the two impropers. They are not the same.
I checked this for dihedrals. Some how the dihedrals from topotools and
unique dihedrals from leap are matching.
So My question is
1. WIll the connectivity of the dihedrals, impropers guessed from bond
topology and the connectivity of the dihedrals, impropers assigned by leap
(based on parametrization, leave out the multi terms or the duplicates)
match always ?
On Sat, Oct 18, 2014 at 7:24 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Hi,
>
> Without more details on how this different tool you are using defines
> impropers, and perhaps a simple of example of how its output differs
> from leap, I don't think we will be able to answer your question.
>
> -Dan
>
> On Sat, Oct 18, 2014 at 3:38 PM, Arun Srikanth <askforarun.gmail.com>
> wrote:
> > Hello amber users,
> >
> > I used parmed.py to get the impropers for my system. From the discussions
> > earlier I understood that the impropers are estimated from bond topology
> in
> > leap based on the definition
> >
> > " an atom shared by three atoms and all three atoms lie on a plane".
> >
> > However if I use some other tool to get the list of impropers for my
> > system. It differs from what leap assigns ?
> >
> > Can you please explain why is this since both use the same definition of
> > impropers. Is it because the tolerance set in estimating whether the
> three
> > atoms are on a plane ?
> >
> > Thanks
> > Arun
> > _______________________________________________
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>
>
>
> --
> -------------------------
> Daniel R. Roe, PhD
> Department of Medicinal Chemistry
> University of Utah
> 30 South 2000 East, Room 307
> Salt Lake City, UT 84112-5820
> http://home.chpc.utah.edu/~cheatham/
> (801) 587-9652
> (801) 585-6208 (Fax)
>
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>
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Received on Sat Oct 18 2014 - 20:30:02 PDT
