Hello GROMACS community, I am a total beginner in using GROMACS, and I’m currently working on a project where I need to simulate the protonation state change of histidine residues in a protein, specifically to simulate an acidic environment where histidines gain a proton (NH3+). I have downloaded a protein structure (1aki.pdb) from the Protein Data Bank, and I’ve followed some online guides to clean the PDB, generate topology files, create a simulation box, and add ions to my system. However, I’m uncertain about how to correctly specify the protonation state and pH conditions in my simulation, and I would greatly appreciate guidance from the experts here. Could you please help me understand the necessary steps and parameters to achieve this protonation state change and simulate an acidic environment (pH =5) ?
At the end i need the .pdb file of the protein in its protonated state to visulize in ChimeraX.
Your assistance would be invaluable to a beginner like me. Thank you in advance!
Protonation states can be set with pdb2gmx. For histidine, use -his to interactively set them to the desired, fully protonated state.
thank you so much for the quick answer, however i was also wondering how i should fill all the minim.mdp files as well as the solvated system (add ions) etc.
Given the complexity of this task and my beginner status. Would it be possible to arrange a brief video call at your convenience? I believe a live discussion would greatly enhance my understanding and allow me to follow the steps more effectively.Your expertise and insights would be invaluable to me, and any assistance you can offer would be greatly appreciated. I am flexible with timings and can adjust to a time that suits you best.