AMBER Archive (2009)

Subject: [AMBER] question about ptraj

From: Jeffrey (
Date: Wed Sep 02 2009 - 03:20:12 CDT

Dear AMBER users,

  I obtained a trajectory of protein solvated in a water box. The simulation was generated by multiple restarts, resulting in mutiple segments of the trajectories. Now I am going to analyze the conformational changes of the protein by PTRAJ.

 In order to reduce the storage space, the solvent was stripped in the merged trajectory by PTRAJ.

trajin npt1.dcd 1 1000 100
trajin npt2.dcd 1 1000 100
trajout merge.dcd netcdf nobox
strip :1000-9999

But how can I get the .prmtop file corresponding to the merged trajectory since other analysis was based on the merged trajectory?

I am not sure whether AMBER can do the job in such a way and request your suggestions.

Many thanks.


Dalian Institute of Chemical Physics, China.

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