that makes sense, thank you Justin<br><br><div class="gmail_quote">On Tue, Jun 1, 2010 at 4:01 PM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<div class="im"><br>
<br>
maria goranovic wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
I tried pdb2gmx with an alanine pdb file, with options 5 (opls force field), 0 (NH3+ n-terminus) and 0 (COO- C-terminus). When I run grompp on the output from pdb2gmx, I get a total charge of -1.1. Any ideas why this happens?<br>
<br>
The same problem is not there if one looks at a dipeptide. Why the problem for a single amino acid? It looks like when pdb2gmx applies patches for the N-terminus and C-terminus to the ends of a protein, it changes atom types for the peptide backbone. If one uses a single amino acid, the patches are applied to the same residue, and hence the odd -1.1 charge? If this is so, is this not a bug?<br>
<br>
</blockquote>
<br></div>
This is not a bug. You're choosing the wrong termini. With OPLS, there is a "zwitterion" terminus option that you should be using, since a single amino acid with two charged termini is a zwitterion.<br><font color="#888888">
<br>
-Justin</font><div class="im"><br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Thank you for inputs,<br>
<br>
-maria<br>
<br>
<br>
-- <br>
Maria G.<br>
Technical University of Denmark<br>
Copenhagen<br>
<br>
</blockquote>
<br></div><div class="im">
-- <br>
========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
<br>
========================================<br>
-- <br></div><div><div></div><div class="h5">
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</div></div></blockquote></div><br><br clear="all"><br>-- <br>Maria G.<br>Technical University of Denmark<br>Copenhagen<br>