patch missing residues

Date: Mon Mar 15 2010 - 15:42:49 CDT

Dear all:

I'm trying to work on a membrane protein, but the PDB file has some
missing residues (~20). I can use MODELLER to add them and construct a
complete structure. But since I have no idea what conformation these
residues would adopt, I started with random loop. It seems to me the
loop would take quite a long time to relax. So my question is: is
there a more elegant way in this situation? Should I perform more
intense minimization, perhaps simulated annealing, before any MD
simulation? If you happen to have a good reference, that would be great.


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