The pull request has been merged. Let me know if you see any problems.
-Dan
On Thu, Mar 26, 2020 at 8:47 PM Kenneth Huang <kennethneltharion.gmail.com>
wrote:
> Hi,
>
> Thanks a lot! It works so far on both deletion systems I have (inosine and
> 2-aminopurine).
>
> Best,
>
> Kenneth
>
> On Thu, Mar 26, 2020 at 3:31 PM Daniel Roe <daniel.r.roe.gmail.com> wrote:
>
> > 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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Received on Fri Mar 27 2020 - 06:30:02 PDT
