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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Hi.<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 lang="EN-US" style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">You don’t have to paste anything in there. Take an empty text document and write the text you like to name your force field like into the first
line. <o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">For example this<o:p></o:p></span></p>
<pre><span lang="EN-US" style="font-size:12.0pt;font-family:"Arial","sans-serif"">GROMOS 53A6 forcefield , extended to include Berger force field parameter.<o:p></o:p></span></pre>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Save it as forcefield.doc. That’s all.<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Good luck!<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><b><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif"">Von:</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>Im Auftrag von </b>Anushree Tripathi<br>
<b>Gesendet:</b> Montag, 23. Januar 2012 08:52<br>
<b>An:</b> Discussion list for GROMACS users<br>
<b>Betreff:</b> Re: [gmx-users] problem in creating forcefield.doc<o:p></o:p></span></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal" style="margin-bottom:12.0pt">I have created one file named it as "forcefield.doc" and paste the contents of "forcefield.itp" into it and also include "lipid.itp file.The content of my "forcefield.doc" file is given below:<br>
<br>
#define _FF_GROMOS96<br>
#define _FF_GROMOS53A6<br>
<br>
[ defaults ]<br>
; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ<br>
1 1 no 1.0 1.0<br>
<br>
#include "ffnonbonded.itp"<br>
#include "ffbonded.itp"<br>
#include "lipid.itp"<br>
<br>
Let me know whether it is correct or not.<o:p></o:p></p>
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<p class="MsoNormal">On Mon, Jan 23, 2012 at 12:17 PM, Mark Abraham <<a href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>> wrote:<o:p></o:p></p>
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<p class="MsoNormal">On 23/01/2012 5:13 PM, Anushree Tripathi wrote: <o:p></o:p></p>
<pre><i>I am using gromacs 4.5.3 version and I am trying to follow the tutorials. For <o:p></o:p></i></pre>
<pre><i> starting I am following the *KALP15 in DPPC* <o:p></o:p></i></pre>
<pre><i> tutorial(<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/02_topology.html" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/02_topology.html</a>). <o:p></o:p></i></pre>
<pre><i><o:p> </o:p></i></pre>
<pre><i><o:p> </o:p></i></pre>
<pre><span style="font-size:12.0pt;font-family:"Arial","sans-serif"">I am not getting the point that is given below :<o:p></o:p></span></pre>
<pre><span style="font-size:12.0pt;font-family:"Arial","sans-serif"">Next, create a </span><code>forcefield.doc</code><span style="font-size:12.0pt;font-family:"Arial","sans-serif""> file that contains a description of the force field parameters in it. Mine contains something like:<o:p></o:p></span></pre>
<pre><span style="font-size:12.0pt;font-family:"Arial","sans-serif""><o:p> </o:p></span></pre>
<pre><span style="font-size:12.0pt;font-family:"Arial","sans-serif""><o:p> </o:p></span></pre>
<pre><span style="font-size:12.0pt;font-family:"Arial","sans-serif"">GROMOS 53A6 forcefield , extended to include Berger force field parameter.<o:p></o:p></span></pre>
<pre><span style="font-size:12.0pt;font-family:"Arial","sans-serif""><o:p> </o:p></span></pre>
<pre><span style="font-size:12.0pt;font-family:"Arial","sans-serif"">Please guide me for creating forcefield.doc.<o:p></o:p></span></pre>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Have a look at the contents of this file in the pre-supplied force fields. Then look at the normal output of pdb2gmx. The former is used in the latter to help you pick the force field you want to use.<span style="color:#888888"><br>
<br>
<span class="hoenzb">Mark</span></span><o:p></o:p></p>
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