Custom Search
--- Neeru On Mon, Dec 12, 2011 at 7:22 PM, David A Case <case.biomaps.rutgers.edu>wrote: > On Sat, Dec 10, 2011, neeru sharma wrote: > > > Actually, I tried to superimpose the topology and coordinate files > > (generated using amber) over my input PDB structure of GDP but they were > > not showing any superimposition. > > As I (tried to) say earlier: this is not necessarily an indication that > anything is wrong. It's not clear how this happened, though, since we > don't > know any of the commands you used to generate the parameters. > > > > > Another amber mailing list member Marc has suggested to use the GDP > > parameters given at: > http://www.pharmacy.manchester.ac.uk/bryce/amber#cof > > But these are in AMBER94 forcefield and I would be using AMBER03 for my > > simulation. So, can I use these parameters for AMBERff03 too or some > > changes are required? > > Opinions differ here. In principle, you might want to use the same charge > derivation method for your "ff03-GDP" parameters as was used in generating > the charges for the protein part of ff03. Such a consistency sounds good, > but doesn't really provide any evidence that the interactions between GDP > and > water/protein parts of your system are actually correct: first, the > deficiencies in the charge distribution using the ff03 procedure might be > different for phosphates than for other types of protein functional groups; > second, the way in which LJ parameters are derived doesn't easily carry > over > to phosphates. > > If you know particular interactions involving the GDP that are important to > you, you might use the published GDP parameters with both ff94 and ff03 and > see how much they differ. > > ....dac > > > _______________________________________________ > AMBER mailing list > AMBER.ambermd.org > http://lists.ambermd.org/mailman/listinfo/amber > -- Regards, Neeru Sharma Project Engineer, Molecular Modelling Team, Bioinformatics Group, Centre for Development of Advanced Computing (CDAC), Ganeshkhind, Pune University Campus, Pune, Maharashtra - 411007 _______________________________________________ AMBER mailing list AMBER.ambermd.org http://lists.ambermd.org/mailman/listinfo/amberReceived on Mon Dec 12 2011 - 07:30:02 PST