<html>
<head>
<meta content="text/html; charset=ISO-8859-1"
http-equiv="Content-Type">
</head>
<body bgcolor="#FFFFFF" text="#000000">
On 11/23/11 4:12 PM, Hu Qiu wrote:
<blockquote cite="mid:001a01cca9b7$9dd8c440$d245c0de@nsiqiuhu"
type="cite">
<meta http-equiv="Content-Type" content="text/html;
charset=ISO-8859-1">
<meta name="Generator" content="Microsoft Word 11 (filtered
medium)">
<o:smarttagtype
namespaceuri="urn:schemas-microsoft-com:office:smarttags"
name="chmetcnv">
<!--[if !mso]>
<style>
st1\:*{behavior:url(#default#ieooui) }
</style>
<![endif]-->
<style>
<!--
/* Font Definitions */
@font-face
{font-family:宋体;
panose-1:2 1 6 0 3 1 1 1 1 1;}
@font-face
{font-family:"\@宋体";
panose-1:2 1 6 0 3 1 1 1 1 1;}
/* Style Definitions */
p.MsoNormal, li.MsoNormal, div.MsoNormal
{margin:0cm;
margin-bottom:.0001pt;
text-align:justify;
text-justify:inter-ideograph;
font-size:10.5pt;
font-family:"Times New Roman";}
a:link, span.MsoHyperlink
{color:blue;
text-decoration:underline;}
a:visited, span.MsoHyperlinkFollowed
{color:purple;
text-decoration:underline;}
span.EmailStyle17
{mso-style-type:personal;
font-family:Arial;
color:windowtext;}
span.EmailStyle18
{mso-style-type:personal-reply;
font-family:Arial;
color:navy;}
@page Section1
{size:595.3pt 841.9pt;
margin:72.0pt 90.0pt 72.0pt 90.0pt;
layout-grid:15.6pt;}
div.Section1
{page:Section1;}
-->
</style>
<div class="Section1" style="">
<p class="MsoNormal"
style="text-align:left;text-autospace:none" align="left"><font
face="Times New Roman" size="3"><span
style="font-size:12.0pt" lang="EN-US">Hi all,<o:p></o:p></span></font></p>
<p class="MsoNormal"
style="text-align:left;text-autospace:none" align="left"><font
face="Times New Roman" size="3"><span
style="font-size:12.0pt" lang="EN-US"><o:p> </o:p></span></font></p>
<p class="MsoNormal"
style="text-align:left;text-autospace:none" align="left"><font
face="Times New Roman" size="3"><span
style="font-size:12.0pt" lang="EN-US">I am
trying to caluculate number of hydrogen bond in my
system using the following
command:<o:p></o:p></span></font></p>
<p class="MsoNormal"
style="text-align:left;text-autospace:none" align="left"><font
face="Times New Roman" size="3"><span
style="font-size:12.0pt" lang="EN-US"><o:p> </o:p></span></font></p>
<p class="MsoNormal"
style="text-align:left;text-autospace:none" align="left"><font
face="Times New Roman" size="3"><span
style="font-size:12.0pt" lang="EN-US">g_hbond
-f model_frame2000.pdb -s md.tpr -n index_water.ndx
-num hbnum.xvg <o:p></o:p></span></font></p>
<p class="MsoNormal"
style="text-align:left;text-autospace:none" align="left"><font
face="Times New Roman" size="3"><span
style="font-size:12.0pt" lang="EN-US"><o:p> </o:p></span></font></p>
<p class="MsoNormal"
style="text-align:left;text-autospace:none" align="left"><font
face="Times New Roman" size="3"><span
style="font-size:12.0pt" lang="EN-US">Where
the file model_frame2000.pdb is the coordinate from a
frame during my MD
simulation, and the index file </span></font><font
face="宋体" size="3"><span
style="font-size:12.0pt;font-family:宋体">（</span></font><font
size="3"><span style="font-size:12.0pt" lang="EN-US">index_water.ndx</span></font><font
face="宋体" size="3"><span
style="font-size:12.0pt;font-family:宋体">）</span></font><font
size="3"><span style="font-size:12.0pt" lang="EN-US">
contains the index six
adjacent tip5p water molecules, see following:<o:p></o:p></span></font></p>
<p class="MsoNormal"
style="text-align:left;text-autospace:none" align="left"><font
face="Times New Roman" size="3"><span
style="font-size:12.0pt" lang="EN-US">2559
2560 2561 2562 2563 3029 3030 3031 3032 3033 3504 3505
3506 3507 3508 <o:p></o:p></span></font></p>
<p class="MsoNormal"
style="text-align:left;text-autospace:none" align="left"><font
face="Times New Roman" size="3"><span
style="font-size:12.0pt" lang="EN-US">5354
5355 5356 5357 5358 5394 5395 5396 5397 5398 6049 6050
6051 6052 6053 <o:p></o:p></span></font></p>
<p class="MsoNormal"
style="text-align:left;text-autospace:none" align="left"><font
face="Times New Roman" size="3"><span
style="font-size:12.0pt" lang="EN-US"><o:p> </o:p></span></font></p>
<p class="MsoNormal"
style="text-align:left;text-autospace:none" align="left"><font
face="Times New Roman" size="3"><span
style="font-size:12.0pt" lang="EN-US">The arrangement
of water oxygen is like this (rectangle), which “ - ”
indicates the distance is
less than 0.35 nm.<o:p></o:p></span></font></p>
<p class="MsoNormal"
style="text-align:left;text-autospace:none" align="left"><font
face="Times New Roman" size="3"><span
style="font-size:12.0pt" lang="EN-US"><o:p> </o:p></span></font></p>
<p class="MsoNormal"
style="text-align:left;text-autospace:none" align="left"><font
face="Times New Roman" size="3"><span
style="font-size:12.0pt" lang="EN-US">OW - OW
- OW<o:p></o:p></span></font></p>
<p class="MsoNormal"
style="text-align:left;text-autospace:none" align="left"><font
face="Times New Roman" size="3"><span
style="font-size:12.0pt" lang="EN-US"> |
| |<o:p></o:p></span></font></p>
<p class="MsoNormal"
style="text-align:left;text-autospace:none" align="left"><font
face="Times New Roman" size="3"><span
style="font-size:12.0pt" lang="EN-US">OW - OW
- OW<o:p></o:p></span></font></p>
<p class="MsoNormal"
style="text-align:left;text-autospace:none" align="left"><font
face="Times New Roman" size="3"><span
style="font-size:12.0pt" lang="EN-US"><o:p> </o:p></span></font></p>
<p class="MsoNormal"
style="text-align:left;text-autospace:none" align="left"><font
face="Times New Roman" size="3"><span
style="font-size:12.0pt" lang="EN-US">The
output hbnum.xvg gives<o:p></o:p></span></font></p>
<p class="MsoNormal"
style="text-align:left;text-autospace:none" align="left"><font
face="Times New Roman" size="3"><span
style="font-size:12.0pt" lang="EN-US"><o:p> </o:p></span></font></p>
<p class="MsoNormal"
style="text-align:left;text-autospace:none" align="left"><font
face="Times New Roman" size="3"><span
style="font-size:12.0pt" lang="EN-US">@TYPE
xy<o:p></o:p></span></font></p>
<p class="MsoNormal"
style="text-align:left;text-autospace:none" align="left"><font
face="Times New Roman" size="3"><span
style="font-size:12.0pt" lang="EN-US">@ view
0.15, 0.15, 0.75, 0.85<o:p></o:p></span></font></p>
<p class="MsoNormal"
style="text-align:left;text-autospace:none" align="left"><font
face="Times New Roman" size="3"><span
style="font-size:12.0pt" lang="EN-US">@
legend on<o:p></o:p></span></font></p>
<p class="MsoNormal"
style="text-align:left;text-autospace:none" align="left"><font
face="Times New Roman" size="3"><span
style="font-size:12.0pt" lang="EN-US">@
legend box on<o:p></o:p></span></font></p>
<p class="MsoNormal"
style="text-align:left;text-autospace:none" align="left"><font
face="Times New Roman" size="3"><span
style="font-size:12.0pt" lang="EN-US">@
legend loctype view<o:p></o:p></span></font></p>
<p class="MsoNormal"
style="text-align:left;text-autospace:none" align="left"><font
face="Times New Roman" size="3"><span
style="font-size:12.0pt" lang="EN-US">@
legend 0.78, 0.8<o:p></o:p></span></font></p>
<p class="MsoNormal"
style="text-align:left;text-autospace:none" align="left"><font
face="Times New Roman" size="3"><span
style="font-size:12.0pt" lang="EN-US">@
legend length 2<o:p></o:p></span></font></p>
<p class="MsoNormal"
style="text-align:left;text-autospace:none" align="left"><font
face="Times New Roman" size="3"><span
style="font-size:12.0pt" lang="EN-US">@ s0
legend "Hydrogen bonds"<o:p></o:p></span></font></p>
<p class="MsoNormal"
style="text-align:left;text-autospace:none" align="left"><font
face="Times New Roman" size="3"><span
style="font-size:12.0pt" lang="EN-US">@ s1
legend "Pairs within 0.35 nm"<o:p></o:p></span></font></p>
<p class="MsoNormal"
style="text-align:left;text-autospace:none" align="left"><font
face="Times New Roman" size="3"><span
style="font-size:12.0pt" lang="EN-US">
-1
4 10<o:p></o:p></span></font></p>
<p class="MsoNormal"
style="text-align:left;text-autospace:none" align="left"><font
face="Times New Roman" size="3"><span
style="font-size:12.0pt" lang="EN-US"><o:p> </o:p></span></font></p>
<p class="MsoNormal"
style="text-align:left;text-autospace:none" align="left"><font
face="Times New Roman" size="3"><span
style="font-size:12.0pt" lang="EN-US">As I
know, the 2nd column is the number of Hydrogen bonds,
and the 3ird column
indicates “the Pairs within 0.35 nm, but with angle >
<st1:chmetcnv tcsc="0" numbertype="1" negative="False"
hasspace="False" sourcevalue="30" unitname="”"
w:st="on">30”</st1:chmetcnv>. After viewing the
stucture in VMD, I found that
the number of Hydrogen bond seems to be correct.
However, only 7 pairs of
water oxygen within 0.35 nm can be found (see above for
the schematic drawing
of water arrangement), thus “the Pairs within 0.35 nm,
but with angle > <st1:chmetcnv tcsc="0"
numbertype="1" negative="False" hasspace="False"
sourcevalue="30" unitname="”" w:st="on">30”</st1:chmetcnv>should
be 7-4 = 3, which is
significantly lower than the value (10) obtained in
hbnum.xvg.<o:p></o:p></span></font></p>
<p class="MsoNormal"
style="text-align:left;text-autospace:none" align="left"><font
face="Times New Roman" size="3"><span
style="font-size:12.0pt" lang="EN-US"><o:p> </o:p></span></font></p>
</div>
</o:smarttagtype></blockquote>
Third column should be simply pairs within 0.35nm, at any angle.<br>
<br>
<blockquote cite="mid:001a01cca9b7$9dd8c440$d245c0de@nsiqiuhu"
type="cite"><o:smarttagtype
namespaceuri="urn:schemas-microsoft-com:office:smarttags"
name="chmetcnv">
<div class="Section1" style="layout-grid:15.6pt">
<p class="MsoNormal"
style="text-align:left;text-autospace:none" align="left"><font
face="Times New Roman" size="3"><span
style="font-size:12.0pt" lang="EN-US">I don't
what's wrong.<o:p></o:p></span></font></p>
<p class="MsoNormal"
style="text-align:left;text-autospace:none" align="left"><font
face="Times New Roman" size="3"><span
style="font-size:12.0pt" lang="EN-US"><o:p> </o:p></span></font></p>
<p class="MsoNormal"
style="text-align:left;text-autospace:none" align="left"><font
face="Times New Roman" size="3"><span
style="font-size:12.0pt" lang="EN-US">Thanks <o:p></o:p></span></font></p>
<p class="MsoNormal"
style="text-align:left;text-autospace:none" align="left"><font
face="Times New Roman" size="3"><span
style="font-size:12.0pt" lang="EN-US"><o:p> </o:p></span></font></p>
<p class="MsoNormal"><font face="Times New Roman" size="3"><span
style="font-size:12.0pt" lang="EN-US">Hu Qiu<o:p></o:p></span></font></p>
</div>
<br>
<fieldset class="mimeAttachmentHeader"></fieldset>
<br>
</o:smarttagtype></blockquote>
<br>
<br>
<pre class="moz-signature" cols="72">--
Gianluca Santoni,
Institut de Biologie Structurale
41 rue Horowitz
Grenoble
_________________________________________________________
Please avoid sending me Word or PowerPoint attachments.
See <a class="moz-txt-link-freetext" href="http://www.gnu.org/philosophy/no-word-attachments.html">http://www.gnu.org/philosophy/no-word-attachments.html</a></pre>
</body>
</html>