[Xplor-nih] Dihedrals Sampling
Ravi Shankar
nahsivar at yahoo.com
Mon Mar 17 12:04:55 EDT 2008
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).
Thanks in advance,
Sivar
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