VMD-L Mailing List

From: Nick Bayhi (bayhi_at_uchicago.edu)
Date: Sat Jul 01 2023 - 17:32:29 CDT

I think you’d need to write the new dcd files out for just the backbone,
but I haven’t done it myself now I’m not 100%.

For me, I have analyzed coarse grained simulations starting from various
cryoEM structures of the same protein but with different N and C termini
cutoffs; I had to save files all trimmed to the same length, in order to
run PCA. That let me analyze them as if it was one long simulation, and I
was able to color my plots differently for the frames that came from each
mutant

On Sat, Jul 1, 2023 at 17:27 Efthymiou, Christos <
christos.dereschuk.20_at_ucl.ac.uk> wrote:

> Hi Nick,
>
> If I create an index file for just the backbone/alpha carbon atoms and use
> the -index option in catdcd, would that work? Or would it still cause an
> error since the input dcd files themselves have different numbers of atoms?
> I am just curious if I need to rewrite the dcd files for each simulation
> just with the backbone or if I can just use the index option to get the
> combined backbone dcd file. Thanks for the help!
>
> Best,
> Christos
> ------------------------------
> *From:* Nick Bayhi <bayhi_at_uchicago.edu>
> *Sent:* Sunday, July 2, 2023 1:13:31 AM
> *To:* Efthymiou, Christos <christos.dereschuk.20_at_ucl.ac.uk>
> *Subject:* Re: vmd-l: Concatenate DCD Files with Different Numbers of
> Atoms
>
>
> ⚠ Caution: External sender
>
> Maybe try to save just the coordinates your your backbone/alpha carbons
> and running pca on that? Should give you the same usable information about
> how the whole protein moves, I’m not sure that pca would be reasonably
> interpretable down to the side chain
>
> On Sat, Jul 1, 2023 at 17:09 Efthymiou, Christos <
> christos.dereschuk.20_at_ucl.ac.uk> wrote:
>
> Hello,
>
> I would like to concatenate some mutant simulations with wild type
> simulations to run PCA analysis. However, catdcd will not allow me to
> concatenate all the simulations into a single DCD file due to the different
> numbers of atoms between the wildtype and mutant as a result of the point
> mutations I introduced. How can I combine these files to run an accurate
> PCA? I have heard that it is necessary to combine all simulations into a
> single file to compare the wildtype and mutant as this ensures PC1, PC2,
> etc. are the same between the various simulations. I appreciate any advice!
>
> Best,
> Christos
>
> --
> --
> Nick Bayhi, (971) 219-7408
> Wei-Jen Tang Lab <https://urldefense.com/v3/__https://voices.uchicago.edu/wtang-lab/__;!!DZ3fjg!6hrYJSgjLJxRHTTjdTXROmCVynR0up_LCsP0fzL66DXh1ImHnvoTgxarhR0293U4YyXYdhgVBF0XE55W_DU$ >
> Biophysical Sciences Graduate Program
> University of Chicago
> 

-- 
--
Nick Bayhi, (971) 219-7408
Wei-Jen Tang Lab <https://urldefense.com/v3/__https://voices.uchicago.edu/wtang-lab/__;!!DZ3fjg!6hrYJSgjLJxRHTTjdTXROmCVynR0up_LCsP0fzL66DXh1ImHnvoTgxarhR0293U4YyXYdhgVBF0XE55W_DU$ >
Biophysical Sciences Graduate Program
University of Chicago