Hello,
Yes, Carlos is right.
In your example, you would rename the "48Z" residue in your PDB file as
"ABB" and then the loaded off and prep files would be used.
Alternatively, you can rename the library files to match the residue you
have.
But by necessity, you'll need to call this something other than DA or DC,
since leap would just build in those entire nucleobases based on those
residue names.
-Christina
On Mon, Mar 30, 2020 at 1:14 PM Carlos Simmerling <
carlos.simmerling.gmail.com> wrote:
> 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.
> >
> > _______________________________________________
> > 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
>
--
-----------------------------------------------------------------
Christina Bergonzo
Research Chemist
Biomolecular Measurement Division, MML, NIST
-----------------------------------------------------------------
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Mar 30 2020 - 11:30:03 PDT
