<div dir="ltr">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> <br> <b> D D 1 0.00000E-00 0.34252E-05</b> ; (D is just the name of my dummy atom)<br>
<br>but got a syntax error when running grompp:<br><b>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</b><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>2) Is [ nonbond params ] the right strategy to the task i described?<br><br>Many Thanks,<br>
Amir<br> <br><br> <br></div>