Hi,
I just implemented a new feature in the GitHub version of cpptraj
(version 6.19.6,
https://github.com/Amber-MD/cpptraj/pull/1037) that
may help you. You'll need to pull the latest version down and
recompile to use it.
There are new keywords, 'specifiedbp' and 'pairs', that allows you to
manually specify base pairing. So for example, with your system you
might use:
nastruct NA naout dna resmap DCP:C resmap D3C:C allhb \
specifiedbp pairs 2-14,3-15,4-16,5-17,6-18,7-19,8-20,9-21,10-22,11-23,12-24
The 'allhb' keyword makes it so that the total number of detected
hydrogen bonds are detected (instead of just the WCF hydrogen bonds,
which is the default behavior). Also by default, parameters will only
be calculated between base pairs when one or more hydrogen bonds are
present. If you want to force the calculation even when no hydrogen
bonds are present you should use the 'calcnohb' keyword as well. Give
it a try and let me know if it works for you.
-Dan
On Mon, Jul 10, 2023 at 11:38 PM Jing Qu <jqu2.ncsu.edu> wrote:
>
> Hi,
>
> I also choose some other options, so my command looks like:
>
> nastruct NA naout nastruct.dat groovecalc 3dna resmap DCP:C resmap D3C:C origincut 15.0 zcut 1.5 zanglecut 30
>
> Is it ok?
>
> The result shows that it counts the base pairs as:
> 1: 2A14A
> 2: 3C15C
> 3: 4G16G
> 4: 7G19G
> 5: 9C21C
> 6: 10G22G
> 7: 11A23A
> 8: 12C24C
>
> And the steps are:
> 1: 2A14A-3C15C
> 2: 3C15C-4G16G
> 3: 9C21C-10G22G
> 4: 10G22G-11A23A
> 5: 11A23A-12C24C
>
> Things got better, though still missing part of the base pairs.
>
> Best,
> Jing
>
> On Mon, Jul 10, 2023 at 10:33 AM Daniel Roe <daniel.r.roe.gmail.com> wrote:
>>
>> 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 Tue Jul 11 2023 - 11:30:02 PDT
