Protonation of nucleic acid phosphates in CHARMM for use in NAMD

From: Hughtendo Martin (
Date: Tue Jul 22 2008 - 08:43:09 CDT


I'd like to inquire into the options I have regarding the protonation of inter-chain and terminal phosphate groups in a nucleic acid chain (P-O- to P-OH). I work with a CHARMM force-field, so if there is some form of patch available (for both single and double protonation in the case of terminal groups), that would be great. If a patch is not available, does anyone have any thoughts on what my options are to attain this goal?

Many thanks,


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