Charles, Thanks for your suggestions. I tried anneal.py from the gb1_rdc directory and this converged to a solution, but the resulting stereochemistry was fairly shaky. In my hands, only distance geometry protocol, followed by simulated annealing, has produced decent results in terms of speed and good stereochemistry. Is there any particular script you recommend for the refinement of DGSA structures?
If there is enough interest on the list, I'll post my experience with homology-derived restraints when some kind of consensus is reached. Cheers, Mensur At 06:53 AM 5/23/2006, you wrote: >Hi Mensur-- > > > I am experimenting with using XPLOR for homology modeling - hope this > > statement does not put off the NMR purists out there :-) When I try to > > use the TAD protocol, it does not converge to any solution even after > > several days. The protein is ~280 residues, and there are > > approximately 9000, 1650 and 125 homology-derived NOE, dihedral and > > h-bonds restrains, respectively. Is this a hopeless case with this > > many restraints, or do I need to change something in the > > nmr_torsion.inp that is provided with the version 2.14? Alternatively, > > what is the smallest subset of homology-derived NOEs that could still > > yield a solution for a protein of this size? I tried using just N-N > > distances, but even that has trouble converging if the distance > > cut-off is 10 A. > >I'm sure you can get this problem to work, but you may have to massage >the parameters a bit. As a start, I'd suggest that you switch to a more >modern starting script- say, one from eginput/gb1_rdc- Of course, you'll >want to remove the references to RDCs. The python interface contains the >most features, so gb1_rdc/anneal.py mist be best to start from. > > > Finally, is there a no-hydrogen topology in present version of XPLOR > > that I can use instead of protein.par? > >Charmm's param19 will do this- param19.pro, and toph19.pro. > >good luck-- >Charles ========================================================================== | Mensur Dlakic, PhD | Tel: (406) 994-6576 | | Department of Microbiology | Fax: (406) 994-4926 | | Montana State University | | | 109 Lewis Hall, P.O. Box 173520 | http://myprofile.cos.com/mensur | | Bozeman, MT 59717-3520 | E-mail: [email protected] | ==========================================================================
