<html xmlns:o="urn:schemas-microsoft-com:office:office" xmlns:w="urn:schemas-microsoft-com:office:word" xmlns="http://www.w3.org/TR/REC-html40">
<head>
<META HTTP-EQUIV="Content-Type" CONTENT="text/html; charset=us-ascii">
<meta name=Generator content="Microsoft Word 11 (filtered medium)">
<style>
<!--
/* Font Definitions */
@font-face
{font-family:"MS 明朝";
panose-1:2 2 6 9 4 2 5 8 3 4;}
@font-face
{font-family:"MS ゴシック";
panose-1:2 11 6 9 7 2 5 8 2 4;}
@font-face
{font-family:Century;
panose-1:2 4 6 4 5 5 5 2 3 4;}
@font-face
{font-family:"\@MS ゴシック";
panose-1:2 11 6 9 7 2 5 8 2 4;}
@font-face
{font-family:"\@MS 明朝";
panose-1:2 2 6 9 4 2 5 8 3 4;}
/* Style Definitions */
p.MsoNormal, li.MsoNormal, div.MsoNormal
{margin:0mm;
margin-bottom:.0001pt;
text-align:justify;
text-justify:inter-ideograph;
font-size:10.5pt;
font-family:Century;}
a:link, span.MsoHyperlink
{color:blue;
text-decoration:underline;}
a:visited, span.MsoHyperlinkFollowed
{color:purple;
text-decoration:underline;}
span.EmailStyle17
{mso-style-type:personal-compose;
font-family:Arial;
color:windowtext;}
/* Page Definitions */
@page Section1
{size:595.3pt 841.9pt;
margin:99.25pt 30.0mm 30.0mm 30.0mm;
layout-grid:18.0pt;}
div.Section1
{page:Section1;}
-->
</style>
</head>
<body lang=JA link=blue vlink=purple style='text-justify-trim:punctuation'>
<div class=Section1 style='layout-grid:18.0pt'>
<p class=MsoNormal><font size=2 face=Arial><span lang=EN-US style='font-size:
10.0pt;font-family:Arial'>Dear all,<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span lang=EN-US style='font-size:
10.0pt;font-family:Arial'>I want to visualize solvent(water) distributions around
one solute molecule.<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span lang=EN-US style='font-size:
10.0pt;font-family:Arial'>I do molecular dynamics calculation with Amber8 program.
<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span lang=EN-US style='font-size:
10.0pt;font-family:Arial'>So I got the following ouput file using grid command of
Ptraj module to analyze trajectories.<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span lang=EN-US style='font-size:
10.0pt;font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span lang=EN-US style='font-size:
10.0pt;font-family:Arial'>This line is ignored<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span lang=EN-US style='font-size:
10.0pt;font-family:Arial'> 1<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span lang=EN-US style='font-size:
10.0pt;font-family:Arial'>rdparm generated grid density<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span lang=EN-US style='font-size:
10.0pt;font-family:Arial'> 100
-49 50
100 -49
50 100 -49
50<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span lang=EN-US style='font-size:
10.0pt;font-family:Arial'>
30.000 30.000
30.000 90.000
90.000 90.000<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span lang=EN-US style='font-size:
10.0pt;font-family:Arial'>ZYX<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span lang=EN-US style='font-size:
10.0pt;font-family:Arial'> -49<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span lang=EN-US style='font-size:
10.0pt;font-family:Arial'>
0.00000 0.00000
0.00000 0.00000
0.00000 0.00000<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span lang=EN-US style='font-size:
10.0pt;font-family:Arial'>
0.00000 0.00000
0.00000 0.00000
0.00000 0.00000<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span lang=EN-US style='font-size:
10.0pt;font-family:Arial'>
0.00000 0.00000
0.00000 0.00000
0.00000 0.00000<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span lang=EN-US style='font-size:
10.0pt;font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span lang=EN-US style='font-size:
10.0pt;font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span lang=EN-US style='font-size:
10.0pt;font-family:Arial'>I think the output is in the format of a XPLOR formatted
contour file and can visualize this output data<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span lang=EN-US style='font-size:
10.0pt;font-family:Arial'>within chimera soft ware. But I don’t know how to treat
this out put file in chimera .<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span lang=EN-US style='font-size:
10.0pt;font-family:Arial'>Can I use this file directory in chimera or have to do
anything else before I use chimera?<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span lang=EN-US style='font-size:
10.0pt;font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span lang=EN-US style='font-size:
10.0pt;font-family:Arial'>Thanks <o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span lang=EN-US style='font-size:
10.0pt;font-family:Arial'>Atsutoshi <o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span lang=EN-US style='font-size:
10.0pt;font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Century><span lang=EN-US><o:p> </o:p></span></font></p>
</div>
</body>
</html>