you can also save a pdb file from leap when you build the system (savepdb),
and then it will be the same orientation as the solvated system.
On Tue, Oct 5, 2021 at 7:05 AM Gao Zhenting <zhentgpicasa.gmail.com> wrote:
> Hi Lin and Anselm,
>
> Thanks for your help.
> I get your point regarding the cpptraj operations.
>
> My goal is to get a solvated box with protein coordinates aligned to the
> original pdb file, before MD simulation.
> Why I want to do this?
> I am learning GIST, and of the tutorial(
> https://ambermd.org/tutorials/advanced/tutorial25/section3.php), solute
> heavy atoms(protein) are restrained, so there is no translational and
> rotational movement during the simulation.
> When it is to define the region for GIST analysis, the ligand is
> co-crystal pdb is used as reference.
> Since the solvated box does not align to the original pdb, I have to
> generated the pdb file of the solvated system(use "ambpdb"), align the
> original PDB to the solvated protein, and then save the coordinates of the
> aligned ligand. This is not a big deal, but if I can have the solvated
> protein aligned to the original pdb at the beginning, then I don't need to
> do all these stuffs.
>
> Any further thoughts?
>
> Regards
> Zhenting
>
> Dr. Anselm Horn <anselm.horn.fau.de> 于2021年10月5日周二 下午4:52写道：
>
> > Hi Zhenting,
> >
> > if solvation changed your coordinates, this should only affect
> > transitions and rotations of your system, but no internal coordinates.
> > Thus, when you simply use the solvated structure as reference for
> > cpptraj analyses of your trajectory results, it should be fine.
> >
> > If you want to check for yourself, that your original pdb structure and
> > the solvated pdb structure are essentially the same, you could also use
> > superimposition and RMSD calculation features in common molecular
> > viewers like VMD or chimera.
> >
> > Regards,
> >
> > Anselm
> >
> > PD Dr.rer.nat.
> > Bioinformatik | NHR.FAU
> > Friedrich-Alexander-Universität Erlangen-Nürnberg
> > Germany
> >
> >
> >
> > Am 05.10.2021 um 06:33 schrieb Song, Lin:
> > > Hi Zhenting,
> > >
> > > You can take a look at the cpptraj tutorials.
> > >
> > > Best,
> > > Lin
> > >
> > >> On Oct 4, 2021, at 11:32 PM, Gao Zhenting <zhentgpicasa.gmail.com>
> > wrote:
> > >>
> > >> Dear Amber users,
> > >>
> > >> After solvating the protein into a box, the original coordinates of
> the
> > >> protein are changed. Is there any way to superpose the solvated system
> > to
> > >> the original pdb structure, so that it is easier to compare the
> > trajectory
> > >> with the original pdb conformation?
> > >>
> > >> Regards
> > >> Zhenting
> > >> _______________________________________________
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> > >> AMBER.ambermd.org
> > >>
> >
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Received on Tue Oct 05 2021 - 04:30:03 PDT
