[gmx-users] Why does protein carry charges?

jadelman at berkeley.edu jadelman at berkeley.edu
Sat May 23 06:18:04 CEST 2009

Hi Lin,

It sounds like you need to look at a basic chemistry or biochemistry
textbook. The protein itself in the PDB shouldn't carry a charge
explicitly until you decide on the pH of your system and assign the
protonation/deprotonation state of residues and add hydrogen atoms
appropriately. While their may be ions in a PDB, most of the time you have
to add them to ensure neutrality for a simulation with Periodic boundary
conditions using PME. I'm not sure what you mean by 'intrinsic counter
ions', but generally people use NaCl or KCl.


> Hi
> I got the protein crystal structures from the PDB file.
> There are only residues and water in the PDB files.
> Why does the protein carry charges?
> Why aren't they electrically neutral?
> What are their intrinsic counter ions ?
> Thank you
> Lin
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