I will give that a go but in the amber tutorial it says: "in early
versions of AMBER it was often necessary to re-image molecules back into
the primary box before calculating RMSd fits. This is no longer necessary
since by default AMBER tracks the original molecule, even if it moves out
of the central box during the course of the simulation " so it shouldn`t be
an issue.
On Thu, 7 Jan 2021 at 22:45, Kenneth Huang <kennethneltharion.gmail.com>
wrote:
> Hi,
>
> Have you tried imaging/centering the molecule to make sure it's not an
> effect of that? Ie, if you had a single protein residue in a water box
>
> parm *.prmtop
> trajin run.nc 1 last 1
> strip :WAT
> center origin :1
> image origin center familiar
> rms first :1.CA,C,N,O
>
> I don't think the RMS fit alone would take care of the imaging/centering
> hence why you get the huge spike, but someone who knows more might have
> insight on that.
>
> Best,
>
> Kenneth
>
> On Thu, Jan 7, 2021 at 5:35 PM K Jan <10dunajkr.gmail.com> wrote:
>
> > Hi Amber users,
> >
> > I`m trying to calculate the RMSD of a 90 ps simulation of a molecule with
> > cpptraj.
> >
> > The rmsd increases from 0 to 17 Angstroms in the 90 ps which is clearly
> too
> > big. I`ve also checked the vmd and my molecule is translating around the
> > screen a small amount and vibrating a little, but the structure of it
> > doesn't change at all, which is strange because the radius of gyration
> has
> > increased, which should mean that the compactness of my molecule has
> > decreased but that hasn`t happened.
> >
> > I read that I have to perform a least-squares fit to remove the global
> > rotation and translation. I am not sure how to do this and would
> appreciate
> > some advice. I read that I could do this on the vmd by using the rmsd
> > trajectory tool but when I try and press align in the tool it says that
> no
> > atoms have been selected, even though I wrote protein in the atom
> selection
> > box, and I have loaded up the topology of my molecule and the trajectory
> > files from my simulation.
> >
> > Would appreciate some help.
> >
> > Thanks ,
> > Kris
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> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
> --
> Ask yourselves, all of you, what power would hell have if those imprisoned
> here could not dream of heaven?
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Received on Thu Jan 07 2021 - 15:30:02 PST
