Well, let me reply to myself.
I have been fiddling with some new functions in cpptraj. here is the one I
have recently noticed and tried, "sscalc".
The manual says "sscalc" is used to derive parameters for single stranded
nucleotides. I gave it a try as follows :
Here is the input I used
parm ../prmtop/mol.prmtop
trajin ../prod/md1.nctraj 1 1000 10
nastruct resmap ABC:U resrange 5,13,6,12,7,11 naout data_6-7 calcnohb
sscalc
run
and the output SS.data_6-7 is
1 1041 5 -nan -nan -nan -nan
-nan -nan
1 5 6 -4.9264 0.5174 -2.6048 -61.2548
-21.7029 -10.6422
1 6 7 3.6622 1.1374 -1.7702 6.5483
-28.2833 -33.2617
1 7 11 2.3931 3.8955 5.5050 -53.9165
-59.4070 -122.6308
1 11 12 -1.8505 1.7534 -3.1038 -42.2589
-4.3030 -1.2110
1 12 13 -4.7211 1.6748 -3.4486 -58.7388
-3.2150 -1.0668
Unfortunately there is no headers describing the columns in the file. I
would appreciate it if an expert out there could address the columns
to ease-up data interpretation.
Regards,
Cenk Andac
On Mon, Jun 13, 2022 at 9:58 PM Cenk Andac <cenkandac.gmail.com> wrote:
> Dear amber community,
>
> I wish to determine roll and twist angles for consecutive base stacking in
> the loop region of a RNA hairpin.
>
> I know that cpptraj uses 'nastruct' to determine many angles between
> consecutive basepairs and basepairs alone. For instance;
> nastruct resrange 1,17,2,16 naout data_1-17_2-16
> will determine the aforementioned angles between basepairs 1:::17 and
> 2::16.
>
> I was wondering 'nastruct' could also be utilized to determine angles
> between a consecutive base stack. If so, how? If not, could you possibly
> let me know if there is another way to do so?
>
> regards,
>
> Cenk Andac
>
>
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Received on Thu Aug 04 2022 - 13:30:47 PDT
