Hi,
Thanks for the quick response- I'm on version V4.25.8 via the Github
branch, and the input is-
> parm HA_ino.prmtop
> trajin curves.nc 1 10 1
> rms first :1-23.P,O5',C5',C4',C3',O3'
> rms :1-46.P,O5',C5',C4',C3',O3'
> rms :1-46./H
> nastruct DNA resrange 1-46 naout nastruct resmap DI:G hbcut 3.5 origincut
> 2.5 zcut 2 zanglecut 65 groovecalc 3dna
>
Which when I run it, errors out with the following mentioning a missing
atom to map with-
ACTION SETUP FOR PARM 'HA_ino.prmtop' (1 actions):
> 0: [nastruct DNA resrange 1-46 naout nastruct resmap DI:G hbcut 3.5
> origincut 2.5 zcut 2 zanglecut 65 groovecalc 3dna]
> Error: Ref Atom [N2] not found in NA base [DI].
> Error: Could not set up residue DI:12 for NA structure analysis.
> Error: Setup failed for [nastruct]
>
I assume this is actually an intended function in since it can't map on the
missing N2, but was wondering if there's workaround to it, ie, map only the
atoms present?
Best,
Kenneth
On Wed, Mar 25, 2020 at 3:42 PM Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Hi,
>
> It would be easier to help if I knew:
>
> 1) The version of cpptraj you are using.
> 2) The exact input you are giving cpptraj
> 3) The exact output you are getting (including the error messages)
>
> Bonus points for sending me off-list a topology and restart I can use
> to reproduce the issue :-)
>
> -Dan
>
> On Wed, Mar 25, 2020 at 2:47 PM Kenneth Huang
> <kennethneltharion.gmail.com> wrote:
> >
> > Hi all,
> >
> > Has anyone had any luck in using nastruct to look at modified base pairs
> > with missing heavy atoms, ie inosine or 2-aminopurine? I've tried using
> the
> > resmap function, but it keeps throwing up a missing atom error flag.
> >
> > Best,
> >
> > Kenneth
> >
> > --
> > Ask yourselves, all of you, what power would hell have if those
> imprisoned
> > here could not dream of heaven?
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Received on Wed Mar 25 2020 - 14:30:02 PDT
