For what it's worth, I seem to recall that the ProDrg server itself warns rather strongly about the charges being unreliable, and I definitely agree with Berk here.
My favorite approach for modeling small molecules is to use the AMBER GAFF small molecule force field in combination with one of the AMBER protein force fields (there are ports for gromacs). The Antechamber package provides a fairly straightforward way to compute sane partial charges for relatively arbitrary small molecules in an automated and fast way. I should really put a tutorial together on this. But unfortunately I'm too swamped at the moment. If anyone wants to volunteer to put together a tutorial, I can provide the web space and some guidance on the steps involved. Best wishes, David On Jan 21, 2008 6:50 AM, Berk Hess <[EMAIL PROTECTED]> wrote: > > > Hi, > > In my opinion the Dundee server produces unreliable charges. > Also it only works for the oldest force field supported in Gromacs. > To obtain proper charges you will have to look in the literature > and if nothing is there, derive charges from quantum calculations > in a way that is compatible with one of the force fields supported > by Gromacs. > > Berk. > > > > Date: Mon, 21 Jan 2008 09:30:20 -0500 > > From: [EMAIL PROTECTED] > > To: [email protected] > > Subject: Re: [gmx-users] Question Regarding Ligand-Enzyme Complex > > > > > I am following the tutorial given in the gromacs manual. While it does > > have a stepwise directions, there is a paucity of detail. The Dundee > > server is part of those directions. > > > > You are right, charge derivation is part of forcefield development. But > > which forcefield does this server use? And unless the forcefield is a > > fully united atom forcefield, the highly positive charge on nitrogen makes > > no sense. And if it is a united atom forcefield - why add hydrogens? If > > the forcefield includes only polar hydrogens, why do amino protons on a > > protonated NH2 group have a negative charge? > > > > These issues are above and beyond a simple read of wth Wiki on gromacs. So > > I again ask what is going on RE: my previous post. > > > > Mark > > > > > > > > All of the above is predicated on your choice of "force field" as a > > model of physics. That server you mention produces topologies in a > > manner (apparently - I know nothing about it) consistent with one such > > force field. The primary source of information about it is the > > publication in which they announced it. You should read about how it was > > developed, and what method that server uses, and form your own > > conclusions. Also, see here > > http://wiki.gromacs.org/index.php/Parameterization > > > > Mark > > _______________________________________________ > > gmx-users mailing list [email protected] > > 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 > > _________________________________________________________________ > Express yourself instantly with MSN Messenger! Download today it's FREE! > http://messenger.msn.click-url.com/go/onm00200471ave/direct/01/_______________________________________________ > > gmx-users mailing list [email protected] > 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 > _______________________________________________ gmx-users mailing list [email protected] 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
