Thank you for your time and the helpful suggestion. I will install the
latest toolbox.
On Fri, Sep 21, 2018 at 9:11 AM Daniel Roe <daniel.r.roe.gmail.com> wrote:
> 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*
> > > > _______________________________________________
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> > > > 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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>
--
*with regards*
*Rajarshi Roy*
*PhD Research Scholar*
*Biosciences and Biomedical Engineering*
*Indian Institute of Technology, Indore*
*India*
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Received on Fri Sep 21 2018 - 10:00:02 PDT
