AMBER TRAJECTORY ANALYSIS

[GoogleCodeExporter]

How to import prmtop, mdcrd (topology file, trajectory file@amber) ?
beccause in MDAnalysis only psf, pdb, dcd/trr. So please provide your answer.

Original issue reported on code.google.com by gschem...@uohyd.ac.in on 16 Feb 2015 at 3:33

[GoogleCodeExporter]

Hi, 

It should automatically detect the format of your files based on their endings, 
so for amber ".top" and ".prmtop" for your topology and ".crd" for the 
trajectory should be recognised.

So:
import MDAnalysis as mda
u = mda.Universe('yourtopology.top','yourtraj.crd')

Original comment by richardjgowers on 16 Feb 2015 at 4:16

[GoogleCodeExporter]

Ah, I made a small mistake there, I meant 'yourtraj.trj'.

It should work with the default file suffix whatever that is.

Original comment by richardjgowers on 16 Feb 2015 at 5:35

[GoogleCodeExporter]

Amber trajectories are supported, see 
https://pythonhosted.org/MDAnalysis/documentation_pages/coordinates/init.html#id
1 and they should be automatically recognized with the "trj" or  "mdcrd" file 
suffix.

Amber topology files are also read 
https://pythonhosted.org/MDAnalysis/documentation_pages/topology/init.html#topol
ogy-readers-mdanalysis-topology with the "top" or "prmtop" suffix.

Please let us know if this works for your example:

  import MDAnalysis
  u = MDAnalysis.Universe('yourtopology.top','yourtraj.mdcrd')

Original comment by orbeckst on 16 Feb 2015 at 5:51

[GoogleCodeExporter]

Hi gschembio,

Could you please let us know if you are now able to read your AMBER 
trajectories, using the suggestions in the comments of this Issue?

If we don't get any feedback we cannot determine if there's a problem and fix 
it. Without feedback I will close the issue in a few days.

Thanks,
Oliver

Original comment by orbeckst on 19 Feb 2015 at 6:07

[GoogleCodeExporter]

I solved it thank you....

Original comment by gschem...@uohyd.ac.in on 20 Feb 2015 at 4:19

[GoogleCodeExporter]

Thanks, then I can close the issue.

Original comment by orbeckst on 20 Feb 2015 at 4:26

• Changed state: Invalid