Yes, Sir, I am trying to use this on protein. I will keep mind on this
On Tue, Apr 30, 2019 at 10:17 PM Pratul Agarwal <pratul.agarwal-lab.org>
wrote:
> To the best of my knowledge, such a functionality is not implemented in
> cpptraj. Others can correct me if I am wrong. Probably easiest to convert
> to GROMACS trajectory, and use gmx analyze.
>
> Also, are you trying to perform this analysis for a protein? If you are,
> be careful. The assumption for such an analysis seems to be "This is useful
> for principal components obtained from covariance analysis, since the
> principal components of random diffusion are pure cosines."
>
> Protein motions are not always harmonic and definitely are not similar to
> random diffusion. Exercise caution, if you are trying to use this as a
> criterion for evaluating the convergence of your MD trajectory.
>
>
> Pratul K. Agarwal, Ph.D.
> (Editorial Board Member: PLoS ONE, Microbial Cell Factories)
> Web: http://www.agarwal-lab.org/
>
>
> On 4/30/2019 12:14 PM, Rajarshi Roy wrote:
>
> Yes. Please check this acs paper and you will get that data in their
> supplementary.
> Exploring Protein Stability by Comparative Molecular DynamicsSimulations
> of Homologous Hyperthermophilic, Mesophilic, andPsychrophilic Proteins
> <https://pubs.acs.org/doi/pdf/10.1021/acs.jcim.6b00305><
> https://pubs.acs.org/doi/pdf/10.1021/acs.jcim.6b00305>
> and also you can check this scientific report paper
> Alanine mutation of the catalyticsites of Pantothenate Synthetasecauses
> distinct conformationalchanges in the ATP binding region
> <https://www.nature.com/articles/s41598-017-19075-2.pdf><
> https://www.nature.com/articles/s41598-017-19075-2.pdf>
>
> On Tue, Apr 30, 2019 at 9:27 PM Pratul Agarwal <pratul.agarwal-lab.org
> ><mailto:pratul.agarwal-lab.org>
> wrote:
>
>
>
> Do you have a reference to a paper, where such a cosine calculation has
> been performed?
>
> Pratul K. Agarwal, Ph.D.
> (Editorial Board Member: PLoS ONE, Microbial Cell Factories)
> Web: http://www.agarwal-lab.org/
>
>
> On 4/30/2019 11:47 AM, Rajarshi Roy wrote:
>
> No Sir. I am talking about the cosine content of the pca projection (not
> dihedral pca), which is also a measure of convergence of the md simulation.
>
> On Tue, Apr 30, 2019 at 6:47 PM Daniel Roe <daniel.r.roe.gmail.com<mailto:
> daniel.r.roe.gmail.com>
>
>
> <mailto:daniel.r.roe.gmail.com><mailto:daniel.r.roe.gmail.com> wrote:
>
>
>
>
>
> Hi,
>
> By "cosine content" do you mean performing principal component
> analysis in dihedral space instead of Cartesian? If so, then yes
> cpptraj can do this. There's even an example in the manual - see
> 'Dihedral covariance matrix calculation' in the 'Analysis Examples'
> section of the cpptraj part of the Amber manual.
>
> If you want to convert to a Gromacs format, use either the command
> line or 'trajout' and convert to 'trr' or 'xtc' format (see manual for
> details).
>
> -Dan
>
> On Tue, Apr 30, 2019 at 1:23 AM Rajarshi Roy <phd1701171011.iiti.ac.in
> <mailto:phd1701171011.iiti.ac.in>
>
>
> <mailto:phd1701171011.iiti.ac.in><mailto:phd1701171011.iiti.ac.in>
>
>
> wrote:
>
>
>
> Dear AMBER users and Development Team,
> I have a query on principal component analysis using cpptraj. Does
>
>
> cpptraj
>
>
> calculate cosine content of the PC? If so, Can we print that data in a
> file? Can it be possible in new ambertools? As we know it can be done in
> gromacs, so which is the best and quick way to convert amber trajectory
>
>
> to
>
>
> gromacs trajectory?
>
> Thank you in advance.
>
> --
> *with regards*
>
> *Rajarshi Roy*
>
>
> *PhD Research Scholar*
>
> *Biosciences and Biomedical Engineering*
>
> *Indian Institute of Technology, Indore*
> *India*
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--
*with regards*
*Rajarshi Roy*
*PhD Research Scholar*
*Biosciences and Biomedical Engineering*
*Indian Institute of Technology, Indore*
*India*
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Received on Tue Apr 30 2019 - 11:00:02 PDT
