Hello, I have recently begun having a problem with my SA script. Here is what I am trying to do: we have fragments of a protein that are oriented with respect to each other. The geometries have been determined with RDCs, I am just using Xplor to correct bad contacts, etc, by minimizing against all my rdcs and a few NOEs. I use the generate script to connect the fragments, which sometimes results in very long bonds. I do a quick minimization to correct these bonds. I then do SA at a very low temp (100K-20K) on only the regions of junctions between fragments. I then do a good long minimization on the whole protein. I no londer do any dynamics at 100K (high T steps = 0) because I don't have enough restraints to re-fold the protein when it unfolds.
I am having 2 major problems: First, I am trying to loop through the SA part 30 times, and it always stops at 12. Second, the structures have recently stopped being random. Meaning, if I do 2 separate runs with different structures as my starting coordinates, the results are always the same- the #1 structures are all identical, the #2 structures are identical, etc. This seems like a very wierd problem that I have never seen before- any suggestions? Thanks, Kristen Kristen L. Mayer, Ph.D. Project Coordinator Southeast Collaboratory for Structural Genomics A126 Life Sciences University of Georgia Athens, GA 30606 phone: 706-583-8192 fax: 706-542-1738 [email protected] -------------- next part -------------- A non-text attachment was scrubbed... Name: sa_011604.inp Type: application/octet-stream Size: 16061 bytes Desc: not available Url : http://dcb.cit.nih.gov/pipermail/xplor-nih/attachments/20040120/ebb87f2d/sa_011604.obj
