From: Natalia Ostrowska (n.ostrowska_at_cent.uw.edu.pl)
Date: Mon Dec 25 2017 - 01:58:35 CST
I think if he can't find a patch for this adduct, he also can't mutate to
this residue bc it's not defined
There are patches defined at the end of parameter files, I would take some
similar patch as an example and start looking for the parameters
Merry Christmas!
Natalia
W dniu niedziela, 24 grudnia 2017 JC Gumbart <gumbart_at_physics.gatech.edu>
napisał(a):
> 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.
>
> Best,
> JC
>
>
> On Dec 24, 2017, at 3:49 AM, The Cromicus Productions <
> thecromicusproductions_at_gmail.com> 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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