Dear Gromacs Users, I have read in previous discussions about different web servers like H++, PDB2PQR, etc., for determining the protonation state of amino acid residues. Still, the problem with them is that pdb2gmx does not identify some of the hydrogen atoms added by those servers. And, if I use the -ignh option, it will ignore all my hydrogens, so no meaning of the protonation is done, and protonation comes to pdb2gmx. My question is, how does pdb2gmx determine the protonation states of residues, I mean, what pH of the system it assumes, or does it consider the local environment of each residue? Also, I want to know how good the predicted protonation states of pdb2gmx are compared to other dedicated web servers made for the same purpose.
Thanks in advance.
Rakesh Srivastava, Ph.D.
IIIT Hyderabad, India.
pdb2gmx assigns protonation states assuming canonical pKa values and a pH of 7. If you have something unusual (e.g. determined by H++ or something else), you need to manually choose the protonation state using the available command-line options. If you have a protonated Asp based on a pKa calculation, pdb2gmx will throw an error about the proton unless you use -asp or -inter to choose the appropriate residue type for it.
Thanks a lot for the clarification.