On Dec 14, 2005, at 5:51 PM, Gregory Zornetzer wrote: > Hi all, > > I've only recently begun using xplor, so I hope this isn't a stupid > question.
Welcome, and not at all. > The results that I'm getting are encouraging - low energies that are > mostly dominated by the NOE term, but Etotals generally less than 100. > Most structures do not have NOE violations. Looking at Etotal is a common mistake. The energies in xplor are physically meaningless--it's simply a function whose value we wish to optimize. In particular, energies are entirely dependent on the values of the various force constants used when the energy is calculated. Looking at the number of NOE violations is much more useful. > At first, I was using top and par files generated by xplo2d from the > HIC-UP database, but more recently, I have generated my own > topology and > parameter files. The main reason for this was to be able to add in > protons. I borrowed atom types from protein.top/par and I used > phosphate parameters from nucleic.par. The new topology/parameter > files > seem to give reasonable structures... I think. > > Couple of questions: > Is there a better script to use as a starting point? Am I biasing my > results (not sampling enough conformational space) using > sa_cross_tor.inp? I'll let Charles answer that, but sampling shouldn't really be an issue. > 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. 3. Make sure your proton names at prochiral centers are correct. 4. Make sure you have enough impropers to define all your chiral centers and planar groups. 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. --JK -------------- next part -------------- An HTML attachment was scrubbed... URL: http://cake.cit.nih.gov/pipermail/xplor-nih/attachments/20051214/9dbfadd6/attachment.html
