Hi Charles, I got a notification from mailing system that I may attach too large file. Here, only the script I used are attached, The pdb and psf files are extended ubiquitin, pdb code 1ubq, generated by xplor-nih.
Thanks! Jie-rong 2009/2/23 Jie-rong Huang <jierongh at googlemail.com> > Hi Charles, > > The attachments are the input files that I used. > > In the emsemble.py, > /TopPar/parallhdg_new.pro and > /TopPar/parnah1er1_mod_new.inp > were copied from xplor-nih 2.20 > > Thanks, > > Jie-rong > > 2009/2/23 <Charles at schwieters.org> > > -----BEGIN PGP SIGNED MESSAGE----- >> Hash: SHA1 >> >> >> Hello Jie-rong-- >> >> > 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 you could send me the exact script you're using, I will try ti >> reproduce your results and figure out what's going on. >> >> best regards-- >> Charles >> -----BEGIN PGP SIGNATURE----- >> Version: GnuPG v1.4.9 (GNU/Linux) >> Comment: Processed by Mailcrypt 3.5.8+ <http://mailcrypt.sourceforge.net/ >> > >> >> iD8DBQFJowWqPK2zrJwS/lYRApUtAJ4hWiGEFVdntzR4f6W0vkDYcuk9LwCfWfik >> f42Fs4Cm07lhXYEixvrA1Og= >> =R7HF >> -----END PGP SIGNATURE----- >> > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://dcb.cit.nih.gov/pipermail/xplor-nih/attachments/20090223/1ba11ac2/attachment.html -------------- next part -------------- A non-text attachment was scrubbed... Name: ensemble.py Type: application/octet-stream Size: 6219 bytes Desc: not available Url : http://dcb.cit.nih.gov/pipermail/xplor-nih/attachments/20090223/1ba11ac2/attachment.obj
