Re: [AMBER] Regarding cosine content calculation in AMBER

From: Rajarshi Roy <phd1701171011.iiti.ac.in>
Date: Tue, 30 Apr 2019 21:44:09 +0530

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>
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>

On Tue, Apr 30, 2019 at 9:27 PM Pratul Agarwal <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> 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>
> 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 - 09:30:01 PDT
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