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 <[EMAIL PROTECTED]>: > 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 > > > Justin A. Lemkul Biochemistry Alpha Chi Sigma, AI '04 Virginia Tech _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
