[AMBER] rmsd and hbond

From: Mary Varughese <maryvj1985.gmail.com>
Date: Mon, 9 Sep 2013 14:50:39 +0530


Is there any need to do a "mass weighted backbone RMS fit of every frame to
the first frame in the trajectory" before performing hbond analysis(by
ptraj). Also on analysing solvent interaction with the system ( dsDNA). is
it sufficient to reimage like (used iwrap=1)

 center :1-20 mass origin// dna
image origin center familiar
center :1-38 mass origin //Na ions
image origin center familiar
center :1-5529 mass origin// water residue
image origin center familiar

 Also if i have to strip water residues at a distance greater than 3.6

would it be ok to have all these in a single script.

I dont want to create another prmtop.

Hbond would be performed on the reimaged trajectory. Isnt?

Thanking you

Mary Varughese
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Received on Mon Sep 09 2013 - 02:30:02 PDT
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