Gromacs pdb2gmx does not alter conformations (though I think charmm has a
toolkit to build at least small molecules from internal coordinates).
pdb2gmx does have an option to add or replace atoms like hydrogens, given
the correct inputs.
On Mon, Dec 4, 2023 at 9:15 AM David A Case via AMBER <amber.ambermd.org>
wrote:
> 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
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Dec 04 2023 - 08:30:03 PST
