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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Received on Tue Oct 05 2021 - 04:30:02 PDT
