vDear Charles,
Thank you very much for your previous reply. The side chain minimization went
well now. Here is another issue, I have an oligomer model generated according
to symmetry. The core of the model is quite crowded due to overlapping of a
helical component. I would like to perform rigid body refinement of the modeled
structure without experimental determined restraints. To do this, I need to fix
the peripheral part of the protomer and group the central alpha helix, allowing
the central alpha helix to move apart from each other during energy
minimization. The script I use is 'sa_mef_dipo.inp' from the eginput/mef_dna.
How should I express the 'fix and group' in this macro? (The expression in
'anneal.py' does not work here.)
Another problem is that during minimization, the central helix should not be
thrown out from the core, can the script achieve this without experimental
restraints? Should I modify the simulation parameter such as temperature, step,
etc. and how?
Thank you very much for your help.
Yi Zhang
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