I am doing the molecular docking and molecular dynamics simulation of protein-ligand interactions. In the first part, I was doing blind docking to find the possible binding sites between protein and ligand.
In order to study the conformational stability of the conformations, I used the docked conformations as the initial conformations in molecular dynamic simulation. Since the ligand could not be recognized by the force field that I chose to treat the protein, can I create the topology files of that ligand (.itp and .gro) files by Prodrg Beta server?
Is it valid to use Prodrg? Is that the same conformations I will get as the earlier dock conformations?
Thank you.
PRODRG parameters lead to serious artifacts.
http://pubs.acs.org/doi/abs/10.1021/ci100335w
You can use it to generate an initial topology that you refine manually, but I have never seen a PRODRG topology that was sufficiently accurate. ATB is a better option, but any server output needs to be inspected and scrutinized. No black-box method is perfect; some are simply better than others.
PRODRG parameters lead to serious artifacts.
http://pubs.acs.org/doi/abs/10.1021/ci100335w
You can use it to generate an initial topology that you refine manually, but I have never seen a PRODRG topology that was sufficiently accurate. ATB is a better option, but any server output needs to be inspected and scrutinized. No black-box method is perfect; some are simply better than others.
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