Quoting Justin Lemkul <[EMAIL PROTECTED]>:
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
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