Re: [NAMD] Question about patches

From: JC Gumbart (
Date: Sun Dec 24 2017 - 15:16:10 CST

You don’t use a patch for this, but rather you use the “mutate” command inside your segment command. Something like

segment XX {
  pdb ____
  mutate RESID 6MA (I think that’s the resname you are talking about)
  first ___
  last ___

Plus whatever patches you need to make it DNA.


> On Dec 24, 2017, at 3:49 AM, The Cromicus Productions <> wrote:
> 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,
> Sebastian

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