Hi Yun,<br><br>Mixed 1-4 scaling of AMBER and GLYCAM requires a trick originally designed for including berger lipids and the OPLS forcefield. I think* the original idea came from Chris Neale and I think there is a paper in detailed in there you should cite. It was recently explained on the GMX list how to adapt it to GLYCAM and AMBER. See here: <a href="http://www.mail-archive.com/gmx-users@gromacs.org/msg43703.html">http://www.mail-archive.com/gmx-users@gromacs.org/msg43703.html</a> <br>
<br>That thread also has links to Chris Neale's original posts. I suggest reading his posts as they explain how it works very well. You will be able to do mixed scaling with reasonable accuracy.<br><br>Best,<br><br>Oliver<br>
<br><div class="gmail_quote">On 19 September 2011 05:44, Yun Shi <span dir="ltr"><<a href="mailto:yunshi09@gmail.com">yunshi09@gmail.com</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;">
Hi Mark and Justin,<br><br>I think I should be more specific here. So i.e., I want to study the interaction between a protein receptor and a carbohydrate ligand with MD simulation, and I plan to use ff99sb for protein while glycam06 for carbohydrate.<br>
<br>Since the two force fields are parameterized using different scaling factors, I should use different fudge values, although these values will not DIRECTLY affect inter-molecular interactions.<br><br>So how to set this up, if it is possible, within .top file and .itp files?<br>
<br>Thanks,<br><font color="#888888">Yun<br>
</font><br>--<br>
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