I hope this message finds you well. I am currently working on a research project focused on MD simulation study of drug desorption behavior on a boron nitride nanosheet with a non-covalent polymer in gromacs . As part of my research, I am facing challenges with the protonation procedure,
Here is a brief overview of the procedure I have been following:
However, I have encountered issues with this procedure. The conversions seem to alter atom types, leading to discrepancies between the atom types in the topology (itp) and gro files, resulting in errors during the simulation.
I would greatly appreciate it if anyone with expertise in this area could share their knowledge and suggest the correct procedure for protonating the system and running MD simulations. Additionally, if you have recommendations for software tools that you have successfully used for drug protonation in similar research, I would be eager to hear your suggestions.
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