AMBER Archive (2009)

Subject: [AMBER] ptraj grid option

From: Youn Kyeung Lee (
Date: Tue Jul 21 2009 - 02:15:11 CDT

I'm trying to check the ion occupancy of the md trajectory file, but all I
got was zero density at every point.
My ptraj file is below

trajin ZNA_WAT.mdcrd
center :1 origin
image origin center familiar
rms first out ':1-12 & !@H='
grid Z_ion.xplor 200 0.5 200 0.5 200 0.5 ':Na+'

I could not understand the "200 0.5 200 0.5 200 0.5" part on the last line.
When I assign 'nx', why do I need 'x_spacing', or when I assign spacing, why
do I need to assign nx?
I guess I misunderstood something on this.
Then, how could I assign this grid point appropriately?
I do not know if this Is the reason that I got wrong result for the ion

I also attach the ptraj file for extracting pdb file which does not contain
the ions.
trajin ZNA_WAT.mdcrd 1 1 1
trajout ZNA_avr.pdb pdb
center :1 origin
image origin center familiar
strip :13-99999999
translate x 0.25 y 0.25 z 0.25

Thank you

Sincerely, YounKyoung_at_Seoul National University
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