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 Justin A. Lemkul Department of Biochemistry 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
