RE: [NAMD] Question about patches

From: Lennart Nilsson (
Date: Mon Dec 25 2017 - 09:17:51 CST

This residue is defined as a complete residue (RESI 6MA) and not as a patch; in this file patches are mainly used for alternative tautomers or protonation states. Just check the supplementary information of the JCC paper, or why not simply have look at the file you are trying to use – “toppar_all36_na_rna_modified.str” is a human-readable text file, and it is quite clear that 6MA is a RESIdue and not a patch (PRES):
toppar_all36_na_rna_modified.str:RESI 6MA -1.00 ! N6-methyladenosine

Good luck!
Lennart Nilsson

From: [] On Behalf Of The Cromicus Productions
Sent: den 24 december 2017 10:49
To: NAMD list <>
Subject: namd-l: [NAMD] Question about patches

Hi everyone,

I'm working with DNA and trying to convert an adenine group into an
N6-methyladenosine. I found the force field from

Xu, Y., K. Vanommeslaeghe, A. Aleksandrov, A. D. MacKerell and L. Nilsson (2016). "Additive CHARMM force field for naturally occurring modified ribonucleotides." Journal of Computational Chemistry 37: 896-912

on one of the latest modifications of CHARMM36 (toppar_all36_na_rna_modified.str) but I'm having problems because there is no patch defined to do this modification and I don't know how to define a patch. Could anyone lead me towards how to perform this task?
I have succeeded before with other modifications such as methylating C bases, but I always had a patch defined in the force field to do this.

Thank you very much and merry Christmas,


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