[AMBER] How to strip water from .mdcrd file?

From: Wujie Wang <wwang02.wesleyan.edu>
Date: Thu, 3 Jul 2014 21:36:13 -0400

Dear fellow AMBER users

I am running a water and ion-explicit DNA simulation. I want to strip all
the water molecules to visualize the simulation. I know cpptraj can help me
remove all the water but do not know how to do it exactly.

I think there may be two way to do it because my purpose is just to
visualize the structure.
1) Strip water from prmtop and mdcrd files.
2) Convert mdcrd to pdb and stip water from pdb file. (This would work
better for my analyzing work) I already know how to convert mdcrd to pdb
but do not know how to strip water and ions from it.

Can anyone tell how to do it or where I can find a document that explains
how to cpptraj.

Thank you!

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Received on Thu Jul 03 2014 - 19:00:02 PDT
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