Changing the pH of protein

User discussions
1

GROMACS version: 5.1.4
GROMACS modification: No
Hello respected community members. I am performing MD simulation of a protein in water. I have changed the protonation state of the titratable amino acids so as to mimick a pH of 4.0. My doubt is that now my system has a charge of 8. Do I need to add counter ions for neutralizing my system?

Thanks in advance.

2

Hi,
Yes you need to neutralise the system. You can use the tool gmx genion to do that.
/Alessandra

4

Just a followup question. Along with the counter ions do I need to add 150 mM of NaCl to mimic the macroscopic salt concentration? Thanks in advance

5

Thanks a lot for answering my question. I was just confused regarding this. I came across a couple of papers where ions were not added to maintain the net charge of protein in low pH. For example: In one paper authors mention that “The net charge of the system was maintained for the pH 5.0 and pH 7.9 structure of T7L after protonation and de-protonation step while the neutral pH structure was neutralized by replacing the water molecules with Cl− and Na+ counter ions based on their net charge”. DOI: 10.1186/s12900-017-0077-9). So that’s why I am confused whether to add ions or not.

6

Hi,
it depends which condition you aim to mimic. 150 mM NaCl is used to mimic a physiological concentration. But for example if you want to mimic see water, then you will use another concentration.
\Alessandra