Hi Yun, Mixed 1-4 scaling of AMBER and GLYCAM requires a trick originally designed for including berger lipids and the OPLS forcefield. I think* the original idea came from Chris Neale and I think there is a paper in detailed in there you should cite. It was recently explained on the GMX list how to adapt it to GLYCAM and AMBER. See here: http://www.mail-archive.com/gmx-users@gromacs.org/msg43703.html
That thread also has links to Chris Neale's original posts. I suggest reading his posts as they explain how it works very well. You will be able to do mixed scaling with reasonable accuracy. Best, Oliver On 19 September 2011 05:44, Yun Shi <yunsh...@gmail.com> wrote: > Hi Mark and Justin, > > I think I should be more specific here. So i.e., I want to study the > interaction between a protein receptor and a carbohydrate ligand with MD > simulation, and I plan to use ff99sb for protein while glycam06 for > carbohydrate. > > Since the two force fields are parameterized using different scaling > factors, I should use different fudge values, although these values will not > DIRECTLY affect inter-molecular interactions. > > So how to set this up, if it is possible, within .top file and .itp files? > > Thanks, > Yun > > -- > 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 >
-- 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
