<div dir="ltr">Thank you Justin,<br><br>I didn't understand though where can I edit the [ nonbond params ] section?<br>Is there a better way to define pairs with no LJ attraction that will ignore the settings in the *nb.itp file?<br>
<br>Cheers,<br>Amir<br><br><div class="gmail_quote">On Mon, Jul 26, 2010 at 5:31 PM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
<div><div></div><div class="h5"><br>
<br>
Amir Marcovitz wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
Hi,<br>
<br>
my system is composed of two molecules, each is composed of a 36 carbon like dummy atoms i defined in the amber files (i.e., has the LJ parameters of a carbon)<br>
I'm interested in eliminating the attractive Lennard-Jones interactions between the dummy atoms , such that only the repulsive terms will account.<br>
<br>
I thought of adding a section to the *.top file: [ nonbond params ] and to set c6 to 0 such that the attractive term of the LJ is eliminated.<br>
I used exactly the same syntax of the tutorial (page 98):<br>
* D D 1 0.00000E-00 0.34252E-05* ; (D is just the name of my dummy atom)<br>
<br>
but got a syntax error when running grompp:<br>
*Fatal error:<br>
Syntax error - File Surface_Surface_1.5_Sep_2.5.top, line 642<br>
Last line read:<br>
'[ nonbond_params ]'<br>
Invalid order for directive nonbond_params*<br>
<br>
1) what is wrong with my syntax? are there any further examples anywhere for the usage of [ nonbond params ] in topology files?<br>
</blockquote>
<br></div></div>
If you have already #included a force field file in the .top, it will have a [nonbond_params] section in it already. You cannot add a new one. The proper approach would be to modify the #included *nb.itp file.<div class="im">
<br>
<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
2) Is [ nonbond params ] the right strategy to the task i described?<br>
<br>
</blockquote>
<br></div>
Sounds like one way to do it.<br>
<br>
-Justin<br>
<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
Many Thanks,<br>
Amir<br>
<br>
<br>
</blockquote>
<br>
-- <br>
========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
<br>
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