Jason Swails
Jason Swails
Interesting... that's too bad. :(
> shoot me an email at ***@***.*** I want a vanity email address, too!
> What immediately appeals to me is to use some toolkit (AMBER tleap or GROMACS tools) to get the protein and ligand into separate parameter files (tleap for the ligand)...
> Good discussion. Minor point: I was looking at the packmol code a while > ago. I think it would be pretty straightforward to wrap, either with f2py > or...
> In terms of pure GROMACS - GROMACS setup has very little support for ligands. So we normally use tleap. However, there are several (probably mostly minor) issues with this....
> Practically, the strategies will likely involve one of two tools in the short term: Either (1) the OpenMM ForceField class, or (2) ParmEd. They have very different advantages. ForceField...
> amber99sbildn.xml does not include uncharged variants of N- and C-terminal residues, though I am not sure if these are yet included in AMBER They are not. > Not quite....
If you are simulating at a pH range of, say, 7 to 10, none of the carboxylate groups will be protonated... ever. So you waste time titrating them. If you...
> I wonder if just stripping the units and caching the unit-stripped values would get us most of that benefit without requiring the SWIG/Cython implementation. If you just make sure...
> * Are we only interested in implementations that let you vary lots of sites at once (e.g. every LYS, ASP, HIS, CYS, and GLU in a large protein)? Or...