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Parameter Set Discussion
Please see the READ BEFORE POSTING topic on how attach longer output segments as .txt files. The scripts used by CHARMM-GUI for model building are somewhat complex and not good examples for a beginner just learning to use CHARMM. Another issue is
Setup, I/O, and Basic questions
Update to most recent CHARMM version.
Energy terms, Constraints, Restraints, and Solvation
Jump to new posts Re: strengthen hydrogen bond by lennart @ 08/21/19 08:32 AM

Your input looks fine to me, so I don't quite know what may be wrong. What does the NOE analysis tell you after the dynamics run? Do you see the NOE energy term increase in the logfile? Can you post a brief, but working, version of your dynamics inp
Parameter Set Discussion
Jump to new posts Re: Parameters for Ammonium ion by lennart @ 08/20/19 03:29 PM

The IC table is not used for any energy calculations, so you don't need it; it can be used for model building, and in this case the 0.0 entries should be filled in using values in the parameter file (see intcor.doc/intcor.info). Eg, if you have coord
CHARMM-GUI
I have not used these parameters, but they appear to be a reasonable starting point.