Hi,
I recommend using the latest version of cpptraj (AmberTools18 or
GitHub) so that you can make use of the 'guessbp' keyword, which is
useful for detecting non-canonical base pairing. The best way to use
it is to strip away everything that you know does't base pair
(potentially including nucleic acids) first. When 'guessbp' is
specified, base pairing will be determined based on selected NA
strands. It is assumed that consecutive strands will be base-paired
and that they are arranged 5' to 3'. The type of base pairing between
strands can be specified with one or more 'bptype' arguments.
For example, I just tested the following on PDB ID 1NK4, which
contains a single G-G mismatch base pair:
parm 1nk4.pdb noconect
trajin 1nk4.pdb
strip !:1-18
nastruct guessbp naout NA.dat
Note how even though there are 19 nucleic acid bases, I can seem from
visualizing the structure that base 19 has no base pairing partner, so
I exclude it.
Hope this helps,
-Dan
On Thu, Sep 20, 2018 at 3:06 PM Rajarshi Roy <phd1701171011.iiti.ac.in> wrote:
>
> Dear Daniel
> I am using amber16 toolbox.
>
> On Thu, Sep 20, 2018 at 7:58 AM Daniel Roe <daniel.r.roe.gmail.com> wrote:
>
> > Hi,
> >
> > What version of cpptraj are you using?
> >
> > -Dan
> > On Tue, Sep 18, 2018 at 1:40 PM Rajarshi Roy <phd1701171011.iiti.ac.in>
> > wrote:
> > >
> > > Dear amber users and developers
> > >
> > > I have a query regarding to *nastruct* command in *cpptraj*. I am
> > > simulating a dsRNA with a single G-G mismatch. But when I was running the
> > > nastruct command, except that mismatch basepair, structural parameters of
> > > other base pairs are shown. Can anyone have any idea about how to fix
> > this
> > > issue?
> > > Thanking you.
> > >
> > > --
> > > *with regards*
> > >
> > > *Rajarshi Roy*
> > >
> > >
> > > *PhD Research Scholar*
> > >
> > > *Biosciences and Biomedical Engineering*
> > >
> > > *Indian Institute of Technology, Indore*
> > > *India*
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> >
> > _______________________________________________
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> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
> --
> *with regards*
>
> *Rajarshi Roy*
>
>
> *PhD Research Scholar*
>
> *Biosciences and Biomedical Engineering*
>
> *Indian Institute of Technology, Indore*
> *India*
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
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Received on Fri Sep 21 2018 - 09:30:02 PDT
