Hi all, I've only recently begun using xplor, so I hope this isn't a stupid question. I am trying to refine the structure of my protein, which includes a covalently bound acyl phosphopantethein species (about 32 heavy atoms, and 20 protons. I have a good-looking structure for the protein, and I want to use xplor to add on the covalently attached species. I was able to use the addUnknownAtoms method to help out with this, though I notice that the structure I get out has a large number of bond, angle, and improper violations. Luckily, this doesn't seem to matter too much, as subsequent refinement seems to clean up the structure.
Once the group is attached, I wanted to refine its structure based on some ambiguous NOE restraints. I've tried using the scripts in eginput/prot_prot as a model, but I've essentially removed the 'fix' statements that held portions of the structure rigid. I also found that the rigid body docking step (rigid_min.inp) wasn't really necessary. (I had modified this step to allow the attachment to be fully flexible.) 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. 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? Are there any hidden or common problems with generating your own topology and parameter files? Thanks very much, -Greg Zornetzer [email protected]
