Hi @scinikhil
If my memory serves me right, that is the top hit that I got doing a search to try to solve this kind of problem.
Could you please do the community, @kj655, and me a favour?
Within that post (that is 17 years old) or any other post:
Could you please specifically point to the solution?
(Not the description of the problem but the solution.)
It seems that knowledgeable scientists over the years have found this atom-naming incompatibility a challenging problem. See for instance this 2021 exchange between @awacha and @jalemkul .
My understanding is that that very conversation lead to a 2023 publication by those two scientists.
The solution proposed in that paper points to a converter on a GitLab page. Unfortunately, the README.md in GitLab says only this:
"
Note: This is work in progress. Do not use this code, not even at your own
risk! The resulting force field is not guaranteed to be correct at all.
On-line documentation: https://awacha.gitlab.io/charmm2gmx
"
In conclusion, for over 17 years people have been reporting this problem. If you could show a documented solution, I and many others would be profoundly grateful to you.
Ivan