Hi,
I've got a pull request in the works that should address your issue:
https://github.com/Amber-MD/cpptraj/pull/806
Once I merge it, try it out and let me know if it works for you.
Seemed to work with the limited testing I did. Cpptraj version will be
V4.25.9 (GitHub).
-Dan
On Wed, Mar 25, 2020 at 5:11 PM Kenneth Huang
<kennethneltharion.gmail.com> wrote:
>
> 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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> >
>
>
> --
> 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 Thu Mar 26 2020 - 13:00:02 PDT
