[AMBER] Problem in Using the Average Command in Cpptraj

From: Robert Molt <rwmolt07.gmail.com>
Date: Mon, 13 Jul 2015 11:38:15 -0400

Good morning,

I am clearly being dense about properly using the average command.

For a teaching purpose, I wanted to show a box of water. I created a
reasonable equilibrated structure from a truncated octahedral "box"
using PBCs. I load the file in cpptraj, specify

center :1-550
image familiar
average Water_550_Average.pdb pdb

The structure I get is a very sparse water box. I obviously am not
imaging properly the water molecules from the "center" box (for lack of
knowing what to call it). My understanding is that "image" puts all
waters in the "center" box, "familiar" is necessary for a truncated
octahedron. Is my mistake obvious to anyone?

Dr. Robert Molt Jr.
Nigel Richards Research Group
Department of Chemistry & Chemical Biology
Indiana University-Purdue University Indianapolis
LD 326
402 N. Blackford St.
Indianapolis, IN 46202
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Received on Mon Jul 13 2015 - 09:00:02 PDT
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