Hi John, Thanks for the advice. On Wed, 14 Dec 2005, John Kuszewski wrote:
<SNIPPED> > > Are there any hidden or common problems with generating your own > > topology > > and parameter files? > It's not too common to generate your own top/par files, but here are > some errors that I've made: > > 1. Chemical type agreement between the parameters & topology. > 2. This goes double for the improper parameters, which are often > defined with wildcard chemical types in the parameter file. Basically, I've used one IMPRoper per tetrahedral center to enforce chirality. I used three impropers to enforce amide planarity, and I've got a thioester in my structure. To make the thioester planar, I used two IMPRopers the par entries are: IMPRoper CT SCO COS O $kpx 0 0.0 IMPRoper CT SCO COS CT $kpx 0 180 where SCO is the thioester sulfur and COS is the thioester carbonyl. I had to define the new COS type in order to get the geometry around the carbonyl right. > 3. Make sure your proton names at prochiral centers are correct. Since I haven't been able to find a PDB structure of this molecule with protons attached, I figure that I've got a carte blanche on the naming, so luckily I don't have to worry about that. > 4. Make sure you have enough impropers to define all your chiral > centers and planar groups. That was tricky. At first I didn't expect to have to make so many restraints, but after staring at a molecular model for a bit, I understood. > In general, if you can take a set of random coordinates, minimize > their covalent energy (bond + angle + improper), > and get a good structure out the end, your top/par set is good. Yep. It looks good. Out of curiosity. Is there a repository for people's top and par files for small molecules besides HIC-UP? Thanks, -Greg
