:)thanks for your help!
I am a beginner of CHARMM. Before I always use AMBER. Exactly because I know very little of how CHARMM works, I don't know whether CHARMM can or cannot do the analysis that I want. I never doubt CHARMM is very powerful,even if it is sort of difficult for the beginner.
Anyway, I learned quite a few things from this. Learning needs some time.
I have another question. Now I would like to simulate a system with nonstandard residues. How should I create their topology and parameter files? Do I need the quantum calculation or just modify the specific part in the rtf file? thanks!