----- Original Message ----- From: priyabrata panigrahi <priyabra...@gmail.com> Date: Thursday, August 26, 2010 17:09 Subject: [gmx-users] Energy minimization by keeping heavy atom fixed To: gmx-users@gromacs.org
> I have a protein structure determined by x-ray crystallography method where > hydrogen atoms were missing. I have added hydrogen atom. Now i need to do > energy minimization of this protein by keeping the heavy atom fixed at their > crystallographic position. How can I manage which atoms to be fixed and which > to keep flexible during EM and MD. The mechanism is called "position restraints" and you should read about that in the manual. pdb2gmx will help generate the necessary file. Mark
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