[gmx-users] sequentially fitting each frame of one trajectory to each frame of another trajectory

[Thomas Evangelidis]

Hi Tsjerk,

Here's the command line:

minVar -s backbone.pdb -f backbone.xtc -log minVar_method3 -out
backbone_minVar+NN.xtc -method 3 -NN 80 -nt_iter 8 -nt 8 -cycle_num 100 -mwa


Thomas


On 17 June 2013 23:37, Tsjerk Wassenaar <tsjerkw at gmail.com> wrote:

> Hey Thomas,
>
> No, there is no such tool. Sorry.
> May I ask how you did the MinVar fitting?
>
> Cheers,
>
> Tsjerk
>
>
>
> On Mon, Jun 17, 2013 at 12:55 PM, Thomas Evangelidis <tevang3 at gmail.com
> >wrote:
>
> > Dear GROMACS list,
> >
> > I used minVar to remove global rotations and translations from a
> > trajectory, but due to memory issues I used a replica with only the
> > backbone of the protein. Now I want to fit each frame of the original
> > protein trajectory to the respective frame of the processed backbone
> > trajectory. Is there any GMX tool that can do that?
> >
> > thanks,
> > Thomas
> >
> >
> >
> > --
> >
> > ======================================================================
> >
> > Thomas Evangelidis
> >
> > PhD student
> > University of Athens
> > Faculty of Pharmacy
> > Department of Pharmaceutical Chemistry
> > Panepistimioupoli-Zografou
> > 157 71 Athens
> > GREECE
> >
> > email: tevang at pharm.uoa.gr
> >
> >           tevang3 at gmail.com
> >
> >
> > website: https://sites.google.com/site/thomasevangelidishomepage/
> > --
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>
>
> --
> Tsjerk A. Wassenaar, Ph.D.
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-- 

======================================================================

Thomas Evangelidis

PhD student
University of Athens
Faculty of Pharmacy
Department of Pharmaceutical Chemistry
Panepistimioupoli-Zografou
157 71 Athens
GREECE

email: tevang at pharm.uoa.gr

          tevang3 at gmail.com


website: https://sites.google.com/site/thomasevangelidishomepage/