Dear Charles, Thank you for the previous replies. I now need to confirm the allowed space for MTSL side chain to move freely. In the other words, after calculated structure with NOE restraints, I substitute a specific residue to CYSP with addatoms.py. Since the generated structure might not be at its lowest energy state and the MTSL side chain could sample a large space, I am thinking about doing energy minimization with fixed backbone atoms. The process should be similar with the preminimization step in AMBER. Which script should I use? Or can I just comment out the restraints and heat-cooling part of the original 'anneal.py' script, then fix the backbone atoms?
Also, is there a simple way to convert MTSL or CYSP parameters (topology, bond, charge, etc.) to AMBER? Thank you very much for your help! Best wishes, Yi Zhang -------------- next part -------------- An HTML attachment was scrubbed... URL: http://dcb.cit.nih.gov/pipermail/xplor-nih/attachments/20101022/92cb7488/attachment.html
