[gmx-users] Ligand Parameters
fyd at q4md-forcefieldtools.org
Tue May 15 08:54:44 CEST 2007
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
Eight charge models are now available...
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