I think Christina was suggesting that you use a new residue name and
library, then the base won't get added.
Look at this paper for an example
Active destabilization of base pairs by a DNA glycosylase wedge initiates
damage recognition
Kuznetsov, N. A., Bergonzo, C., Campbell, A. J., Li, H., Mechetin, G. V.,
de los Santos, C., Grollman, A. P., Fedorova, O. S., Zharkov, D. O.,
Simmerling, C., Nucleic Acids Research, 2015, 43 (1), 272-281
DOI: 10.1093/nar/gku1300
On Mon, Mar 30, 2020 at 1:08 PM Robert Molt <rwmolt07.gmail.com> wrote:
> Good afternoon,
>
> I am very appreciative for the parameter suggestion, but unless I am
> confused, I do not see that it addresses the question I asked? I am
> confused about how to "leave a space" properly, and use the existing
> parameters?
>
> On 3/30/20 11:07 AM, Christina Bergonzo wrote:
> > Hello,
> >
> > In the past (the way past - 2011!) we have used these parameters:
> > https://www.ncbi.nlm.nih.gov/pubmed/17323932
> >
> > Kun Song created these leap files while in Carlos Simmerling's lab.
> > I attached the off and frcmod files to this email, as well as a picture.
> >
> > Please make sure they are compatible with any changes to the DNA FF since
> > 2007!
> >
> > -Christina
> >
> > On Mon, Mar 30, 2020 at 10:36 AM Robert Molt <rwmolt07.gmail.com> wrote:
> >
> >> Good morning,
> >>
> >> I am attempting to simulate abasic DNA with a protein "bonded" to said
> >> DNA structure. In particular, an amino acid ends up "occupying" the
> >> "empty" location of the abasic DNA.
> >>
> >> In attempting to figure out the best way to construct this in Amber, I
> >> found the following post:
> >>
> >> http://archive.ambermd.org/201901/0211.html
> >>
> >> in which Dr. Case elaborates that one might "remove the base from A,
> >> replacing it with a hydrogen."
> >>
> >> I think I have a misunderstanding of how leap works for which I seek
> >> clarification.
> >>
> >> I have a "residue" named 48Z which is the phosphate backbone in my
> >> crystal structure associated with the abasic site. I think I have to
> >> "name" this residue something akin to "DA" or "DC" in order to tell leap
> >> to connect the phosphate backbone properly (it expects to connect the
> >> polymer). But to my understanding, the act of doing so will
> >> automatically tell leap to fill in the missing heavy atoms? This seems
> >> to be the behavior when I attempt this.
> >>
> >> --
> >> Dr. Robert Molt Jr.
> >>
> >>
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
> --
> Dr. Robert Molt Jr.
>
> _______________________________________________
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>
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Received on Mon Mar 30 2020 - 10:30:03 PDT
