David, Thank you for the quick and detailed reply. I thought that the analog approach would be a bit too quick-and-dirty, anyway :-) I will set to work on making some new parameters based on the information you've provided, and I will likely focus on compatibility with the GROMOS force fields. Perhaps I will have something useful to contribute in due time. Thanks for the link to the script; I know it will prove most useful.
Thanks agin, Justin Quoting David Mobley <[EMAIL PROTECTED]>: > Justin, > > > 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 :-) > > Are you committed to a particular force field? For example, with > PRODRG, you are stuck with GROMOS or whatever else it can output > (hence, you would need to use the same force field for other elements > in the system).. Also, the charges from there would have, (ahem), > possible issues even if it would generate parameters for your > molecule. For example, their FAQ page says, > > "Q: The atomic charges don't always come out right? A: This is a well > known limitation. PRODRG works with the concept of charge groups, > which are defined as a group of bonded atoms with an integer charge. > E.g. -COO would have the C (with a slight positive charge) and the two > O's (with an equal negative charge) in one "charge group" with the > total charge being -1. Thus in order for PRODRG to assign atomic > charges it needs to be able to recognise the charge groups first. This > is particularly difficult in ring systems with nitrogens, and several > charge group definitions (e.g. C-Cl) or still missing. I would > definitely recommend that you check these charges before starting your > 2 microsecond simulation." > > In other words, you can't count on the charges to be right (for > example, this charge groups concept is rather questionable). > > As far as having worked with O+, I haven't. You could try running it > through antechamber (specifying the -nc flag for your molecule) and > see if it actually can generate parameters for it... If you can > parameterize it with Antechamber, you can use our conversion script > (http://www.alchemistry.org/FreeEnergyTools) to convert those to > GROMACS format (for use with the AMBER ports to GROMACS). But I can't > vouch for how Antechamber will work for something with O+. > > > 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. > > Have you searched the literature? If there aren't O+ parameters in > current force fields, I suppose you'll have to derive them yourself in > a manner consistent with the force field you plan on using for the > rest of your system (i.e. possibly from QM). > > > 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? > > Presumably dihedrals, etc are affected by the atom types, > hybridization, etc. Sounds like a bad idea. If I were a reviewer on a > paper that did this, I'd probably think it was an even worse way to > parameterize something than the "make the parameters up based on > chemical intuition" approach. > > The way to do this: Figure out what force field you want to use; look > up how existing parameters for that force field were derived, and then > do something consistent with that to get your new parameters. The > procedure will be different depending on the force field you want to > use. > > Best wishes, > David > _______________________________________________ > 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 > 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
