On Fri, Nov 18, 2011 at 8:07 PM, Mark Abraham <mark.abra...@anu.edu.au> wrote: > On 19/11/2011 6:42 AM, Ben Reynwar wrote: >> >> On Fri, Nov 18, 2011 at 7:23 AM, Mark Abraham<mark.abra...@anu.edu.au> >> wrote: >>> >>> On 18/11/2011 8:10 AM, Ben Reynwar wrote: >>>> >>>> Dear gromacs list, >>>> >>>> Does anyone know how well current force fields capture the energetics >>>> of non-specific protein-protein interactions? I'm simulating a >>>> protein with an arm that alternates between (apparently) non-specific >>>> adsorption to the main-body of the protein and free movement in the >>>> solvent. Can I place any trust in the results of an MD simulation for >>>> something like this? I haven't seen any comparison of experimental >>>> results with simulation results of the energetics of non-specific >>>> protein-protein interactions so I'm a little skeptical about it. >>>> Currently I'm using generalized born implicit solvent, which is >>>> perhaps a mistake when solvation energies could be critical to the >>>> results. >>>> >>> I'd be very skeptical unless you can observe many adsorption/desorption >>> processes and with explicit solvent (though they're probably mutually >>> exclusive). >>> >>> Mark >> >> I think I asked my question poorly. >> In a perfect simulation with explicit solvent and infinite sampling, >> roughly what kind of error might one expect for peptide-peptide >> interaction energies due to the force field? >> Presumably there are papers out there that go into this, but I'm not >> finding them. If anyone knows of any directions to point me in, I'd >> really appreciate it. > > I don't recall having ever seen an explicit solvation simulation on even a > small peptide that claimed exhaustive sampling, never mind a system that > shows such complex behaviour. It's possible someone has used slow-growth > methods to grow a small peptide ligand onto the side of a protein, and that > could give a guide to the accuracy of inter-protein energetics, but I've > never gone looking for such. > > Mark
Cool. Thank you. I think I need to spend some quality time with the parameterisation literature. > -- > 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
