Hi everybody,<br><br>I want to use pdb2gmx command to create a .gro file and a .top file for PAMAM whose repeat unit is amidoamine ( attached ).<br><br> /<br>---CH2--CH2--CO-NH-CH2-CH2-N (see the attached figure)<br>
\<br><br>The atom N have two same branches with --CH2--. I write the rtp file for it as follows:<br><br> [ atoms ]<br> C1 opls_245 -0.050 1 <br> .........<br> [ bonds ]<br>
C1 -N7<br>.......<br> C6 N7<br><span style="color: rgb(255, 0, 0);"> N7 +C1</span><br style="color: rgb(255, 0, 0);"><span style="color: rgb(255, 0, 0);"> N7 +C1</span><br><br>It seems not work, which gives a wrong top structure. The question is how can I deal with the two branches of N. Any suggestion is appreciated. <br>
<br>Thanks in advance.<br><br><br>-- <br>wende<br>