Problems in setting up low pH systems

From: Sheng, Zi-Zhang (
Date: Wed Jan 11 2012 - 09:43:31 CST

Dear all,

I am a new learner of NAMD. I want to simulate a protein under low pH. I used PDB2PQR to assign the protonation state to pH5 first. The .pqr file generated by PDB2PQR is used for generating psf file in VMD using autopsf. The output of VMD shows that there are two charges in the system, but PDB2PQR shows that there are three. It seems VMD will delete the protonation state generated by PDB2PQR and reassign them by itself. How can i avoid of this? And also, is it appropriate or enough to setup low pH system simply by assigning protonation state and adding neutral ions to the system? Is it necessary to change HIS to HSE when modeling low pH system?

Thank you.

Zizhang sheng

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