On Mon, Dec 04, 2023, Fadaei Fatemeh Mgr. wrote:
>
>According to the NAB manual, bdna() utilizes a uniform helical step of
>3.38° rise and 36.0° twist. My confusion arises from the fact that I
>recently created DNA with 90 base pairs using the NAB tool, resulting in a
>helical turn of 9 and a helical twist of 36 degrees.
I believe the bdna parameters come from very old fibre diffraction data. If
you want different helical parameters, you can modify them.
>My main query revolves around the use of the parmbsc0 force field. If I
>intend to use the parmbsc0 force field, will the average twist be changed
>to 33 degrees automatically after using pdb2gmx in GROMACS? If so, in this
>case, will the helical turn be adjusted to 8.25, and will the structure be
>altered?
I am not a GROMACS user, but my understanding is that pdb2gmx does not alter
the input structure, which is used as the starting structure for an MD
simulation. In principle, running a simulation using parmbsc0 would yield
(after some time) an average structure for a given force field that is
similar to those reported in the literature.
...hope this helps....dac
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Received on Mon Dec 04 2023 - 08:30:03 PST
