Dear Charles, I used a modified script from dna_refi/ensemble.py, in which only BOND, ANGL, IMPR, VDW energies are considered, to test how the random conformers look like.
The size of ensemble for 1 and 8 were tested. As you suggested before, the larger the size of ensemble, the longer dynamics needed. However, even if the dynamics for 8 conformer is set up to 12 ps (at each cooling temperature, default in the original script was 0.2 ps), the radius of gyration of 8 conformer is much smaller than the results from 1 conformer. I would expect the outcome of calculation without experimental restraint should be independent of the size of ensemble. (It doesn't change this phenomenon if RAMA is added. ) If look at the PDB files, random conformers for the size of 8 are locally more compacted. You mentioned that the setting of "rcon" and "repel" may be tricky, is this the problem? If I didn't describe clearly, I can upload those PDB files. Thanks! Best wishes, Jie-rong -------------- next part -------------- An HTML attachment was scrubbed... URL: http://dcb.cit.nih.gov/pipermail/xplor-nih/attachments/20090223/b3c3fdd4/attachment.html
