Recently I had posted a question about measurement of water T1.
I got tons of very useful replies, a gist of which I will soon post here.
This time I have a different question to ask, about protocols for structure
calculation using NMR constraints.
Recently we performed solution NMR experiments on a short
20 residue peptide and obtained several (mostly intra-residue and
between consecutive ones with a few long distance in the sequence) NOE
peaks which can qualitatively be classified as strong, medium and weak.
Now we are ready to perform structure calculations using these constraints.
We don't have any dedicated NMR suite (DYANA, X-PLOR etc.) so we
would like to work with the Discover module in InsightII that is available here.
I would like to know some standard protocols for doing structure calculations
using the Discover module. I am looking for specific protocols like what
starting structure to use, how to do the simulated annealing (how long, how
fast and to what temperature), protocols for cooling down, final energy
minimization, when should the constraints be turned on, what force constants
one should use, how to generate a series of structures, how to choose
the better ones etc. We are not after generating high resolution
structure, rather, we want to have some reasonable conformations to
begin with.
cheers,
Gautam Basu
Calcutta
5 May 1999