[gmx-users] PCA analysis results

[Nithyanan Annamalai]

Dr Tsjerk,

Thank you for your explanation.

The PDB model I used in this simulation was obtained from I-TASSER.
There is no ligand involved.

Dr, may I know what would be the optimal/ suggested simulation time for
this protein with 567 aa?

On Sat, Dec 19, 2015 at 4:06 AM, Tsjerk Wassenaar <tsjerkw at gmail.com> wrote:

> Hi Nithyanan,
>
> Right. So now we have that clear, I've had a look at the PDB file :p
> What you see is the result of filtering over a single eigenvector. You
> protein is kind of curling up through rotations of domains. You can't
> describe these rotations with a single eigenvector. They will be dispersed
> over multiple, and you will need at least two to capture the rotations.
> Maybe there's a twist associated and then you'd surely need one more.
>
> As an aside, looking at the trajectory confirms me that this is a
> relaxation motion. I don't know whether you removed a ligand and this is a
> functional relaxation, or that is was started from a crystal structure, but
> it is something to be aware of.
>
> Hope it helps,
>
> Tsjerk
>
> On Fri, Dec 18, 2015 at 8:51 PM, Nithyanan Annamalai <
> nithyanny90 at gmail.com>
> wrote:
>
> > Hi Dr Tsjerk,
> >
> > I didn't do any clustering or make it whole.
> >
> > I just use the .xtc that I ontained after the simulation since I found
> out
> > there is no pbc effect of the protein.
> >
> > On Sat, Dec 19, 2015 at 3:42 AM, Tsjerk Wassenaar <tsjerkw at gmail.com>
> > wrote:
> >
> > > Hi Nithyanan,
> > >
> > > How did you preprocess the trajectory? Did you cluster and/or make
> > > everything whole?
> > >
> > > By the way, 50 ns is probably too short for a protein of that size. It
> > will
> > > probably still be relaxing and the eigenvectors will be those of the
> > > relaxation.
> > >
> > > Cheers,
> > >
> > > Tsjerk
> > >
> > > On Fri, Dec 18, 2015 at 8:34 PM, Nithyanan Annamalai <
> > > nithyanny90 at gmail.com>
> > > wrote:
> > >
> > > > Dear GROMACS users,
> > > >
> > > > I have performed 50ns MD for 567 aa monomer protein using gromos53a6
> ff
> > > in
> > > > explicit water in the cubic box with 2fs time step.
> > > >
> > > > I have  used g_covar and g_anaeig to perform Principal Component
> > > Analysis/
> > > > Essential Dynamics analysis.
> > > >
> > > >
> > > > But when I view the animation of the trajectory it, the movement of
> the
> > > > protein looks weird.
> > > >
> > > > Can anyone please help to explain to me what I can do to get the
> right
> > > > trajectory?
> > > >
> > > > Link for eigenvalue file:
> > > >
> > > >
> > > >
> > > >
> > >
> >
> https://drive.google.com/file/d/0B2PnnS1LZvokVS10N0dDTXFWRGM/view?usp=sharing
> > > >
> > > > I have used the following command line to extract the results:
> > > >
> > > >
> > > > g_anaeig -f ../../md_0_1.xtc -s ../../md_0_1.tpr -n ../../index.ndx
> -v
> > > > ../../phac_monomer_50ns_wild_Protein_eigenvec.trr -eig
> > > > ../../phac_monomer_50ns_wild_Protein_eigenval.xvg -filt
> > > mono_wild_filt1.pdb
> > > > -rmsf mono_wild_PC1_eigrmsf.xvg -first 1 -last 1 -skip 100
> > > >
> > > > pdb file link:
> > > >
> > > >
> > > >
> > >
> >
> https://drive.google.com/file/d/0B2PnnS1LZvokbzdqN1VvVWtxUU0/view?usp=sharing
> > > >
> > > >  g_anaeig -f ../../md_0_1.xtc -s ../../md_0_1.tpr -n ../../index.ndx
> -v
> > > > ../../phac_monomer_50ns_wild_Protein_eigenvec.trr -eig
> > > > ../../phac_monomer_50ns_wild_Protein_eigenval.xvg -extr
> > > > mono_wild_extreme1.pdb  -first 1 -last 1 -nframes 50
> > > >
> > > > pdb file link:
> > > >
> > > >
> > >
> >
> https://drive.google.com/file/d/0B2PnnS1LZvokSE5OMUZLbGl4MDA/view?usp=sharing
> > > > --
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> > >
> > > --
> > > Tsjerk A. Wassenaar, Ph.D.
> > > --
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>
> --
> Tsjerk A. Wassenaar, Ph.D.
> --
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