On Dec 16, 2005, at 11:53 AM, Gregory Zornetzer wrote:
> 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. Technically, prochiral protons should have the same numbering that a methyl carbon would have in that same position. Read what IUPAC has to say: Pure & Appl. Chem., Vol. 70, No. 1, pp. 117-142, 1998. But note that xplor's names traditionally don't follow IUPAC rules, in order to make name matching via wildcards easier. If you do something arbitrary with the names, you should note that clearly in any PDB files you create, in order to keep the poor database people from going over to the dark side. > 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. Great. One last common error, which you've probably already taken care of, is ensuring that the equilibrium bond angles and impropers are consistent with each other--you want to be able to take the system down very close to zero covalent geometry energy. In planar groups, it's trivial to make the bond angles add up to 360 degrees around each atom. But around chiral centers, it's a bit more of a headache. What I've done is started with an initial guess at the value of the chiral center improper, minimized with bonds + angles + impropers (to get me into the neighborhood), then minimized again with just bonds + angles (to ensure that they're not stretched at all), and then read off the equilibrium value of the improper with a pick dihedral statement. Out of curiosity. Is there a repository for people's top and par files for small molecules besides HIC-UP? I don't know of anything really great, esp with protons. This is a perennial headache for the NMR community. Charles and I have discussed a few possibilities, but it's a rather large job. --JK -------------- next part -------------- An HTML attachment was scrubbed... URL: http://cake.cit.nih.gov/pipermail/xplor-nih/attachments/20051216/8217a9b5/attachment.html
