CHARMM Development Project Forums User Discussion & Questions Setup, I/O, and Basic questions read multiple rtf/prm for NA, PROT, LIPID, CHOL

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To solve your problem, you have to renumber the MASS statements in the topology file, copy-paste them into a new "ATOM" section in the parameter file, and read the resulting parameter files with the flex keyword. Please read this discussion thread carefully (including the second page) for a discussion on the subject.

We're currently in the process of reorganizing the CHARMM force field distribution. All the force fields will have non-overlapping MASS numbers and will be compatible with the flexible parameter reader. That should make these kind of annoyances a thing of the past. We're planning to release the new CHARMM force field distribution next week.