Hi Jing,
Thanks for the files. I have 2 things for you to try. First, your DNA
contains a non-standard protonated cysteine (residue DCP), the name of
which 'nastruct` doesn't recognize by default. You can add 'resmap'
keywords to map non-standard residues back to recognized nucleic acid
templates, e.g.
resmap DCP:C resmap D3C:C
I need to add a warning to cpptraj to make it clear when 'resmap'
might be needed.
Also, the default cutoffs that 'nastruct' currently uses to determine
base pairing haven't been well-tested on non-WC base paired
structures. Try using values that are closer to what 3DNA uses:
origincut 15.0 zcut 1.5 zanglecut 30
So in summary, your 'nastruct' command should look something like:
nastruct NA naout dna resmap DCP:C resmap D3C:C \
origincut 15.0 zcut 1.5 zanglecut 30
Try that and let me know how it looks.
-Dan
On Fri, Jul 7, 2023 at 2:00 PM Daniel Roe <daniel.r.roe.gmail.com> wrote:
>
> On Fri, Jul 7, 2023 at 11:49 AM David A Case via AMBER
> <amber.ambermd.org> wrote:
> >
> > I think Dan is correct about needing to see a structure. Parallel strand
> > duplexes may have never been tested, and it's not hard to imagine that they
> > could fool an algorithm trying to find "Watson-Crick" base pairs.
>
> The base pair determination algorithm was recently updated (version
> 6.18.0 https://github.com/Amber-MD/cpptraj/pull/1018), so in theory
> non-WC base pairing should also be detected (which can be the case in
> e.g. Z-DNA, G-quadruplexes etc). However, the new "better"
> determination method is only about 4 months old so there is probably
> still room for improvement.
>
> -Dan
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Received on Mon Jul 10 2023 - 08:00:02 PDT
