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On 23/01/2012 6:49 PM, Anushree Tripathi wrote:
<blockquote
cite="mid:CAAx43BwcqGqjRvB3CcJFoJp2YVs6oKdPahjFUKEV9Wc7pTBTwg@mail.gmail.com"
type="cite">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.<br>
</blockquote>
<br>
No, it isn't.<br>
<br>
Mark<br>
<br>
<blockquote
cite="mid:CAAx43BwcqGqjRvB3CcJFoJp2YVs6oKdPahjFUKEV9Wc7pTBTwg@mail.gmail.com"
type="cite"><br>
<div class="gmail_quote">On Mon, Jan 23, 2012 at 12:17 PM, Mark
Abraham <span dir="ltr"><<a moz-do-not-send="true"
href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex">
<div bgcolor="#FFFFFF" text="#000000">
<div>
<div class="h5"> On 23/01/2012 5:13 PM, Anushree Tripathi
wrote:
<blockquote type="cite">
<pre><i>I am using gromacs 4.5.3 version and I am trying to follow the tutorials. For
</i><i> starting I am following the *KALP15 in DPPC*
</i><i> tutorial(<a moz-do-not-send="true" 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>).
</i><font face="Arial"><font size="3">I am not getting the point that is given below :
Next, create a <code>forcefield.doc</code> file that contains a description of the force field parameters in it. Mine contains something like:
GROMOS 53A6 forcefield , extended to include Berger force field parameter.
Please guide me for creating forcefield.doc.
</font></font></pre>
<br>
</blockquote>
<br>
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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 class="HOEnZb"><font
color="#888888"><br>
<br>
Mark<br>
</font></span></div>
<br>
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