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
---------------------------------
Never miss a thing. Make Yahoo your homepage._______________________________________________
Xplor-nih mailing list
[email protected]
http://dcb.cit.nih.gov/mailman/listinfo/xplor-nih
