Hi Charles, For comparison reason, I would like to run grid_search.inp to get Da and Rh. I have used several softwares to estimate Da and Rh for a same set of pdb and rdc data. From Module, I got Aa=-6.31, Rh=0.313, and from calcTensor.py and got Da=-8.16, Rh=0.314. I have managed to get grid_search.inp run smoothly, but I am not sure if I set parameters correctly. I would like to set initial Da=-8.16 and variy it -15 in a step 0f 0.5 and Rh=0.31 variy it in a step of 0.02 to 0.41. The attached is the script, could you please to go through it?
By the way, I wonder if water refinement has been done in either anneal.py or refine.py? seem not! Best wishes, Hongyan Quoting Charles at Schwieters.org: > -----BEGIN PGP SIGNED MESSAGE----- > Hash: SHA1 > > > Hello Hongyan-- > > > I got a similar problem as Michael's and I obtained a CYANA structure > > and input in xplor-NIH and refined by RDC and NOE constraints started > > from initial cyana structure. I used calTensor.py to calculate the Da > > and Rh for the lowest structure (10.14, 0.467) and using these as > > initial tensor and allow tensor to be varied. I calculated 100 > > structures and analysis of 50 structures showed many violations on > > noe, VDW. And Surprising Da and Rh values varied a lot, particularly > > Da varied from ca. 30 to ca. -22, does it make sense? Any suggestions > > will be highly appreciated! > > In this case, it's probably best to determine values of Da and Rh from > the distribution and only allow them to vary during final minimization > (ala gb1_rdc/anneal.py) > > best regards-- > Charles > -----BEGIN PGP SIGNATURE----- > Version: GnuPG v1.4.6 (GNU/Linux) > Comment: Processed by Mailcrypt 3.5.8 <http://mailcrypt.sourceforge.net/> > > iD8DBQFF/wUgPK2zrJwS/lYRAl78AJ9aIw953rph9Z6PIk1qRdLHfkz3PwCfQFWO > 0dF09rlvu56M3rli7xZtS8Y= > =4ofc > -----END PGP SIGNATURE----- > Dr. Hongyan Li Department of Chemistry The University of Hong Kong Pokfulam Road Hong Kong -------------- next part -------------- A non-text attachment was scrubbed... Name: grid_search.inp Type: application/octet-stream Size: 2739 bytes Desc: not available Url : http://dcb.cit.nih.gov/pipermail/xplor-nih/attachments/20070320/ef2fbaaa/attachment-0001.obj
