[gmx-users] Ligand Parameters

Justin Lemkul jalemkul at vt.edu
Mon May 14 18:32:22 CEST 2007

Hello all,

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?

Thanks in advance for any insights!


Justin A. Lemkul
Department of Biochemistry
Virginia Tech

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