Justin, The GFP protein consist of chromophore group which matured after folding of that protein. That prostetic group is the cyclized derivative of the Ser-Tyr-Gly peptide which is the part of the alpha-helix of that protein surrounded by the beta-barell interiour.
So I want to make simulation of such protein consisted of covalently bonded prostetic group. I've made parametrisation of that isolated chromophore but couldn't integrate it into GROMOS force field because aminoacids.rtp didnt work with ITP file produced by PRODRG. It's also inportant that different mutants of GFP consist of different types of that chromophores so manual conversion of the ITP to RTP formats in each cases ( I'd like to simulate different mutants) would be very routinely. James 2012/12/5 Justin Lemkul <jalem...@vt.edu>: > > > On 12/5/12 11:00 AM, James Starlight wrote: >> >> Hi Bharat, >> >> That simulation have been done in charmm program so the convertion >> from charmm to gromacs would be more routinely for me. >> >> > > I think it would be better if you describe exactly what you need help with. > If it's a matter of having parameters in CHARMM format but not Gromacs > format, then all you need is to follow the manual to implement the > parameters. If you're having a specific problem along the way, please > describe it fully and specifically, otherwise the default response is > "everything's in the manual and elaborated on at the webpage you already > quoted." > > -Justin > > -- > ======================================== > > Justin A. Lemkul, Ph.D. > Research Scientist > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > > -- > 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
