I wish to study the change in interaction of the small molecule with the protein in respective to change in pH. GROMACS focuses most on protonation state and not directly on pH. So how can I proceed my study?
Thirumal Kumar GROMACS achieves studying "different pHs" by assigning different protonation states. You can run independent trajectories (each w/ its own tpr) using different protonation states for residues which have a pKa near that pH.
As for dynamically changing charges on a protein during a trajectory, constant pH molecular dynamics simulations in NAMD and CHARMM can achieve that, maybe others, but not GROMACS to my knowledge.
Thirumal Kumar GROMACS achieves studying "different pHs" by assigning different protonation states. You can run independent trajectories (each w/ its own tpr) using different protonation states for residues which have a pKa near that pH.
As for dynamically changing charges on a protein during a trajectory, constant pH molecular dynamics simulations in NAMD and CHARMM can achieve that, maybe others, but not GROMACS to my knowledge.
Very useful discussion, @Thirumal Kumar.
I'll also try do proceed for the same as told by thr experts.
Hi
JD Tamucci is correct. The pH is only involve in the protonation states. You can use web servers like H++, Proppka, and pdb2pqr to assign the protnation states at different pH and carry out MDs in the normal way.
You can try amber package that supports simulations at different pHs
http://ambermd.org/tutorials/advanced/tutorial18/index.htm
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