Dear researcher,
I am a learner of Gromacs. I want to simulate my protein in different pH. in .mdp file i did not saw any option to define the pH.
please suggest me how can i set the pH
You don't. You set a dominant protonation state representative of a given pH using options in pdb2gmx to alter the protonation state of titratable residues based on their individual pKa values.
It is not possible to define pH in an MD system as there are no hydronium ions floating around (you can't plausibly model that) and protons can't be exchanged in classical MD, anyway.
You don't. You set a dominant protonation state representative of a given pH using options in pdb2gmx to alter the protonation state of titratable residues based on their individual pKa values.
It is not possible to define pH in an MD system as there are no hydronium ions floating around (you can't plausibly model that) and protons can't be exchanged in classical MD, anyway.
I would suggest to look into constant-pH MD methods. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3114466/, http://www.cell.com/biophysj/abstract/S0006-3495(05)72666-7?cc=y=. Protonation states could, as a brute force manner, be defined statically based on the pKa value using propka : http://nbcr-222.ucsd.edu/pdb2pqr_2.0.0/ Best, Emanuel
You can use pdb2gmx to alter the protonation state of titratable residues based on their individual pKa values as stated by Justin Lemkul. for example, suppose your protein is named protein.pdb, you can use command below to interactively determine the protonation states of all titratable residues in your protein
pdb2gmx -f protein.pdb -inter
You can read more about other options to use for protonation of specific residues by typing the command below at your linux terminal.
pdb2gmx -h
Hi Rohit, take a look at the ProteinPrepare web application (www.playmolecule.org). Its uses PROPKA3.1 for protonation prediction (residue titration at your desired pH) plus PDB2PQR for H-bond network optimization. You can then download results and optimized structure (PDB) for simulation.
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