Hello, I am attempting to generate force-field parameters for a fatty acid molecule that contains a carboxilic acid head group. I decided to use the parameters for stearic acid as the base for my molecule, since they contain similar structures with the only major change being a shorter hydrophobic tail. I noticed that the charge on stearic acid, and other molecules that have a carboxilic head group, is spread out with -0.9 residing on the head group and -0.1 on the second carbon. I need to use the protonated from of my molecule for my simulation, as well as the deprotonated form. I looked into the parameters for the COOH replacement in the Charmm27 force-field and used that to form the head group of the protonated form of my molecule. The problem that I am facing is that this left behind a charge of -0.1 that resides on the second carbon. Is there any way to find acceptable partial charges without doing the full Gaussian calculations? I would also appreciate it if someone could explain why the charges were split onto the second carbon in the first place.
Thanks in advance, Eric Stokes -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
