[gmx-users] Help with respect to processing protein with FE2+

Prasanth G, Research Scholar prasanthghanta at sssihl.edu.in
Mon Dec 24 16:12:07 CET 2018

Dear all,

One of the proteins of my interest, has a FE2+ in the center and as it
plays a main role in the activity of the protein, it cannot be removed.
Can you please suggest a solution. I have tried with CHARMM and GROMOS,
with no success.

After reading a bit, I understood that, the charges on the ions cannot be
represented effectively as we generalized the residues as spheres and ions
cannot be represented with such a generalization. But, i have not found any
solution as to how to edit the protein.pdb file, so that the program
accepts it.
Hoping that someone can help me with this.
Wishing you and your family a Merry Christmas.


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