[gmx-users] Ligand Parameters

[Justin Lemkul]

Thanks to all for sharing thoughts.  I will keep the list apprised of any
successes; it may be useful to others down the road.

-Justin

Quoting FyD <fyd at q4md-forcefieldtools.org>:

> Quoting Justin Lemkul <jalemkul at vt.edu>:
>
> > I am interested in simulating some small molecules that involve oxygen in
> > aromatic rings (which thus bears a +1 charge).  I tried to submit
> > one of these
> > molecules to PRODRG, but got an error indicating that there were too
> >  many bonds
> > to O.  I thought this issue might arise, due to the unusual condition of
> the
> > oxygen (+1 charge, hybridization, etc.)  I have looked into the list
> >  to see if
> > anyone had come across a similar problem, but I can't find an
> > explicit example.
> >  I realize this odd case is probably limited by the developed force field
> > parameters, which don't appear to include O+.  I have checked the
> > *.atp entries
> > to confirm this.  I read on the archive that it might be possible to
> develop
> > parameters using the ffamber ports (which I have) and using
> > ANTECHAMBER (which
> > I have used) to get partial charges.  I would then have to create
> > some entries
> > in the applicable .rtp file, etc, and otherwise do a lot of reading
> > in Chapter
> > 5 of the manual :-)
> >
> > I realize this problem is not trivial, and I don't expect an easy
> > solution, but
> > I was wondering if anyone out there had worked with O+ in their
> > molecules, and
> > if they had any advice or topology building blocks that I might use as a
> > template, seeing as none have been contributed online.
> >
> > I have also considered submitting an analog of my compound to PRODRG
> (normal
> > aromatic ring instead of one containing O+) to get the dihedrals,
> > etc. and then
> > re-calculating charges under ANTECHAMBER.  Any thoughts on that approach?
>
> You might want to try to use the RESP ESP charge Derive (R.E.D.)
> version III - http://q4md-forcefieldtools.org/RED/.
> You can generate RESP or ESP charge values for molecules and molecule
> fragments.
> Eight charge models are now available...
>
> regards, Francois
>
>
>



Justin A. Lemkul
Biochemistry
Alpha Chi Sigma, AI '04
Virginia Tech