AMBER Archive (2009)

Subject: [AMBER] question about ptraj

From: Jeffrey (jeffry20072008_at_yahoo.cn)
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.

e.g.
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.

Jeffrey 

----
Dalian Institute of Chemical Physics, China.

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