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Hello Ravi- > I want to do a sampling(partial) of dihedral angles space for a given > protein using Xplor-NIH. I am totally new to it and am not familiar > with NMR terminologies [ I don't have to use them, atleast for now ]. > I understand that, to Xplor, one can just feed a dihedral constraints > file and an extended initial structure and do a SA to reach > somewhere. I just want to do this (which sounds simple) but getting > started with Xplor doesn't seem to be easy :-( . I have some MD > experience and am familiar with topology , parameters file, energy > minimization etc., yet even with the good examples in the tutorials > directory, without much NMR knowledge I am not able to achieve an > understanding to be able to do a rather simple thing I want with > Xplor. Please help. Is there any flowchart describing the process of > generating a structure from a sequence using Xplor [ I wasn't able to > find one ]. Simply, with the protG example from the eginput > directory, how do i use Xplor to randomly sample the dihedrals > space. [just for the phi and psi ] using a constraint of + or - 20 deg > taken from the solved, native PDB structure and with no other > constraints). I'm not exactly certain of what you are trying to do, but if you're looking at eginput/protG/anneal.py you can turn off all energy terms except for CDIH and run the calculation with a new dihedral table. Use the format of protG_dih.tbl (which is described here: http://nmr.cit.nih.gov/xplor-nih/doc/current/xplor/node181.html ) You will want to disable all covalent minimization (using the minc variable), and also fix the omega angle by specifying fixedOmega=True in the arguments of torsionTopology. I don't think you'll get a very good structure, but I hope this helps. best regards-- Charles -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.6 (GNU/Linux) Comment: Processed by Mailcrypt 3.5.8+ <http://mailcrypt.sourceforge.net/> iD8DBQFH3r0sPK2zrJwS/lYRAmhgAJsGYL8c2niGmBB7i+9EiNHfsnhn8gCfemS2 gB0EfsGuKN1T+QphvxLwDGk= =CwVW -----END PGP SIGNATURE-----
