Hi Mark,<br><br>Thanks for your reply. But, I do not know the meaning of the columns in specbonds.dat. I also do not find any information in the manual 4.0. <br><br>Could you provide something about the specbonds.dat or give some explanations.<br>
<br>Thanks in advance.<br><br><br><br><div class="gmail_quote">2010/10/9 Mark Abraham <span dir="ltr"><<a href="mailto:mark.abraham@anu.edu.au">mark.abraham@anu.edu.au</a>></span><br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<div><div></div><div class="h5"><br><br>----- Original Message -----<br>From: lammps lammps <<a href="mailto:lammp2forum@gmail.com" target="_blank">lammp2forum@gmail.com</a>><br>Date: Saturday, October 9, 2010 19:27<br>
Subject: [gmx-users] how to write a rtp file for amido amine<br>To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a>><br><br><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font>Hi everybody,<br>
<font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font><br><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font>I want to use pdb2gmx command to create a .gro file and a .top file for PAMAM whose repeat unit is amidoamine ( attached ).<br>
<font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font><br><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font> /<br>
<font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font>---CH2--CH2--CO-NH-CH2-CH2-N (see the attached figure)<br><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font> \<br>
<font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font><br><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font>The atom N have two same branches with --CH2--. I write the rtp file for it as follows:<br>
<font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font><br><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font> [ atoms ]<br>
<font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font> C1 opls_245 -0.050 1 <br><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font> .........<br>
<font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font> [ bonds ]<br><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font> C1 -N7<br>
<font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font>.......<br><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font> C6 N7<br>
<span style="color: rgb(255, 0, 0);"><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font> N7 +C1</span><br style="color: rgb(255, 0, 0);"><span style="color: rgb(255, 0, 0);"><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font> N7 +C1</span><br>
<font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font><br><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font>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></div></div>pdb2gmx is intended only for work with linear heteropolymers. Any more complex things (e.g. disulfides, branched structures) have to be engineered using the specbonds.dat mechanism.<br><font color="#888888"><br>
Mark
</font><br>--<br>
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