On 6/15/16 11:34 AM, Nikhil Maroli wrote:
Hi, I saw that already. in yasara software, they assign the protonation states of amino acids and ligands depending on the chosen pH.i know that that classical MD does not include dissociation and reassociation of protons, so residues will not change their protonation states during the MD. possibility in gromacs ?
You can change protonation states using pdb2gmx. See the help information on how to do it, or the previous threads on this same topic (there are many, even recently).
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