<html xmlns:v="urn:schemas-microsoft-com:vml" xmlns:o="urn:schemas-microsoft-com:office:office" xmlns:w="urn:schemas-microsoft-com:office:word" xmlns:m="http://schemas.microsoft.com/office/2004/12/omml" 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 12 (filtered medium)">
<style>
<!--
/* Font Definitions */
@font-face
{font-family:Helvetica;
panose-1:2 11 6 4 2 2 2 2 2 4;}
@font-face
{font-family:Helvetica;
panose-1:2 11 6 4 2 2 2 2 2 4;}
@font-face
{font-family:Calibri;
panose-1:2 15 5 2 2 2 4 3 2 4;}
@font-face
{font-family:Tahoma;
panose-1:2 11 6 4 3 5 4 4 2 4;}
/* Style Definitions */
p.MsoNormal, li.MsoNormal, div.MsoNormal
{margin:0cm;
margin-bottom:.0001pt;
font-size:12.0pt;
font-family:"Times New Roman","serif";}
a:link, span.MsoHyperlink
{mso-style-priority:99;
color:blue;
text-decoration:underline;}
a:visited, span.MsoHyperlinkFollowed
{mso-style-priority:99;
color:purple;
text-decoration:underline;}
span.EmailStyle17
{mso-style-type:personal-reply;
font-family:"Calibri","sans-serif";
color:#1F497D;}
.MsoChpDefault
{mso-style-type:export-only;}
@page Section1
{size:612.0pt 792.0pt;
margin:72.0pt 72.0pt 72.0pt 72.0pt;}
div.Section1
{page:Section1;}
-->
</style>
<!--[if gte mso 9]><xml>
<o:shapedefaults v:ext="edit" spidmax="1026" />
</xml><![endif]--><!--[if gte mso 9]><xml>
<o:shapelayout v:ext="edit">
<o:idmap v:ext="edit" data="1" />
</o:shapelayout></xml><![endif]-->
</head>
<body lang=EN-US link=blue vlink=purple>
<div class=Section1>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>Coordinate files like pdb and gro aren’t used by GROMACS to
provide any bonding information. That is what the topology files are for. So
their “presence” in your pdb isn’t an issue.<o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'><o:p> </o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>Actually, what is probably happening is that PyMol is guessing
the bonds presence, based on the distance between atoms, and displaying it
(which is what VMD does as well). So the bonds aren’t actually there at all in
the pdb file.<o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'><o:p> </o:p></span></p>
<p class=MsoNormal><span style='font-size:10.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>Catch ya,<br>
<br>
Dr. Dallas Warren<br>
</span><span style='font-size:10.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>Drug Delivery, Disposition and Dynamics</span><span
style='font-size:10.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><br>
</span><span style='font-size:10.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>Monash Institute of Pharmaceutical Sciences</span><span
style='font-size:10.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>,
Monash University<br>
381 Royal Parade, Parkville VIC 3010<br>
dallas.warren@pharm.monash.edu.au<br>
+61 3 9903 9167<br>
---------------------------------<br>
When the only tool you own is a hammer, every problem begins to resemble a
nail.</span><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'> <o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'><o:p> </o:p></span></p>
<div style='border:none;border-left:solid blue 1.5pt;padding:0cm 0cm 0cm 4.0pt'>
<div>
<div style='border:none;border-top:solid #B5C4DF 1.0pt;padding:3.0pt 0cm 0cm 0cm'>
<p class=MsoNormal><b><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'>From:</span></b><span
style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'>
gmx-users-bounces@gromacs.org [mailto:gmx-users-bounces@gromacs.org] <b>On
Behalf Of </b>Gunnar Widtfeldt Reginsson<br>
<b>Sent:</b> Thursday, 12 November 2009 10:13 AM<br>
<b>To:</b> gmx-users@gromacs.org<br>
<b>Subject:</b> [gmx-users] Docking with PyMol and using Gromacs<o:p></o:p></span></p>
</div>
</div>
<p class=MsoNormal><o:p> </o:p></p>
<p class=MsoNormal>Hi.<o:p></o:p></p>
<div>
<p class=MsoNormal>I am a new user of Gromacs.<o:p></o:p></p>
</div>
<div>
<p class=MsoNormal><o:p> </o:p></p>
<div>
<p class=MsoNormal>My question is both PyMol and Gromacs related.<o:p></o:p></p>
</div>
<div>
<p class=MsoNormal>I tried the PyMol users mailing list but couldn't find
anything.<o:p></o:p></p>
</div>
<div>
<p class=MsoNormal>I have a small organic molecule that I am inserting into DNA
in pymol.<o:p></o:p></p>
</div>
<div>
<p class=MsoNormal>I have the DNA as one pdb file and the organic molecule as
another pdb file. I open the DNA file in pymol and then load the organic
molecule. After docking the organic molecule I write "save name.pdb"<o:p></o:p></p>
</div>
<div>
<p class=MsoNormal>When viewing the name.pdb file in pymol there are some bonds
between the organic molecule and the DNA that I don't want. Somehow pymol
creates them and I don't see those bonds in the name.pdb file when I open it in
a text reader.<o:p></o:p></p>
</div>
<div>
<p class=MsoNormal><o:p> </o:p></p>
</div>
<div>
<p class=MsoNormal>I then create a .gro file with pdb2gmx of the DNA.pdb and a
.gro file of the organic molecule with topolbuilder 1.2 , and unite those .gro
files and convert into a .pdb with editconf <o:p></o:p></p>
</div>
<div>
<p class=MsoNormal>The newly created pdb file still has those unwanted
bonds. <o:p></o:p></p>
</div>
<div>
<p class=MsoNormal><o:p> </o:p></p>
</div>
<div>
<p class=MsoNormal><o:p> </o:p></p>
</div>
<div>
<p class=MsoNormal>My question is:<o:p></o:p></p>
</div>
<div>
<p class=MsoNormal>Can I ignore those bonds?<o:p></o:p></p>
</div>
<div>
<p class=MsoNormal>If not, how can I prevent pymol making those bonds?<o:p></o:p></p>
</div>
<div>
<p class=MsoNormal><o:p> </o:p></p>
</div>
<div>
<p class=MsoNormal><o:p> </o:p></p>
</div>
<div>
<p class=MsoNormal>Thanks.<o:p></o:p></p>
</div>
</div>
</div>
</div>
</body>
</html>