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Hi,<br>
<br>
see here for a start:<br>
<br>
<a class="moz-txt-link-freetext" href="http://www.gromacs.org/Documentation/How-tos/Parameterization">http://www.gromacs.org/Documentation/How-tos/Parameterization</a><br>
<br>
<br>
Cheers,<br>
<br>
Jochen<br>
<br>
<br>
On 10/8/10 Oct 8,3:51 PM, lammps lammps wrote:
<blockquote
cite="mid:AANLkTinJcOM7Zgtk35YnOiWGhTXaEq+2xSpHWnHmneYk@mail.gmail.com"
type="cite">
<div class="gmail_quote"><br>
Hi everybody,<br>
<br>
I want to use OPLS-AA force field to do simulation for
dendrimer(see the attached files for figure and .pdb). If the
pH<4.0£¬the tertiary amines on the dendrimer will be
protonated, i.e. (CH2)3-N will be changed to (CH2)3-NH+. Now, I
have two questions as follows.<br>
<br>
1. How can I use pdb2gmx to get the .gro and .itp? It seems
there are not the <i>residue.</i><br>
<br>
2. I don't find the suitable force field for the N in
(CH2)3-NH+, How can I deal with this?<br>
<br>
Any suggestion is appreciated. Thanks in advance.<br clear="all">
<br>
-- <br>
wende<br>
<br>
</div>
</blockquote>
<br>
<br>
<pre class="moz-signature" cols="72">--
---------------------------------------------------
Dr. Jochen Hub
Computational and Systems Biology
Dept. of Cell & Molecular Biology
Uppsala University. Box 596, 75124 Uppsala, Sweden.
Phone: +46-18-4715056 Fax: +46-18-511755
<a class="moz-txt-link-freetext" href="http://xray.bmc.uu.se/~jochen/index.html">http://xray.bmc.uu.se/~jochen/index.html</a>
---------------------------------------------------
</pre>
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