I second Justin here, for Amber FF (which share essentially the same topology but with different parameters with OPLS/AA), the impropers dihedrals seems to be enough as for TRP.<div><br></div><div>Just a side note, using ACPYPE (which uses antechamber in the core) to generate topologies for molecules like TRP, 6 extra impr. dihedrals are added, but clearly not necessary.</div>
<div><br></div><div>You may want to try ACPYPE as I believe antechamber does a really good job getting the topology (even if in excess of imp. dih as for TRP and probably for <span style="font-family:arial, sans-serif;font-size:13px;border-collapse:collapse">napthalene<span style="border-collapse:separate;font-family:arial;font-size:small">), and of course check the literature as suggested by Justin.</span></span></div>
<div><br></div><div>Alan</div><div><br><div class="gmail_quote">On Wed, Apr 28, 2010 at 06:13, <span dir="ltr"><<a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div>Ming Han wrote:<br>
> 1__2 6__<br>
> // 3\/ \\<br>
> | ||4 |<br>
> \\___ /\___//<br>
> 5 7<br>
><br>
><br>
> I want to know if 1-2-3-6 torsion should be included?<br>
> And if both 2-3-4-7 and 6-3-4-5 should be included?<br>
> Thanks.<br>
><br>
<br>
I would think that proper dihedrals would not even be used for such a molecule.<br>
The fused ring systems will utilize impropers to stay planar. For example,<br>
the TRP side chain specifies no proper dihedrals within the indole side chain;<br>
only impropers are used, but maybe someone with more OPLS derivation experience<br>
can comment.<br>
<br>
You can also look into the literature. A simple Google search for "napthalene<br>
OPLS" (without the quotes) turns up tons of simulation papers.<br>
<br>
-Justin<br></div></blockquote></div><br><br clear="all"><br>-- <br>Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate<br>Department of Biochemistry, University of Cambridge. <br>80 Tennis Court Road, Cambridge CB2 1GA, UK.<br>
>><a href="http://www.bio.cam.ac.uk/~awd28" target="_blank">http://www.bio.cam.ac.uk/~awd28</a><<<br>
</div>