<br><br><div class="gmail_quote">On Sat, Mar 14, 2009 at 10:03 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="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
<div class="im"><br>
<br>
Ilya Chorny wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
I created a new ffoplsaa.rtp entry for ASN with a polysacharide attached to the side chain nitrogen called ASBG. I want to test the new residue by itself.<br>
<br>
When I pdb2gmx it I get the following error.<br>
<br>
-------------------------------------------------------<br>
Program pdb2gmx, VERSION 4.0.3<br>
Source code file: pgutil.c, line: 87<br>
<br>
Fatal error:<br>
Atom N not found in residue 1094904186 while adding improper<br>
<br>
-------------------------------------------------------<br>
<br>
</blockquote>
<br></div>
If the residue is by itself, something is seriously wrong if pdb2gmx is detecting a billion residues!</blockquote><div><br></div><div>I'll checkmy file again. </div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
<div class="im"><br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
If I comment out <br>
CA +N C O improper_O_C_X_Y<br>
<br>
</blockquote>
<br></div>
Right, because if the residue is by itself, there will be no N in the next residue (+N).</blockquote><div><br></div><div>If this is true then pdb2gmx will crash evertime it is run on an isolated AA, which it doesn't. <br>
</div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;"><div class="im"><br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Then pdb2gmx creates the gro and top with no error messages.<br>
<br>
I saw an much earlier post by Justin with a similar error message but no resolution. Anyone have anythoughts?<br>
<br>
</blockquote>
<br></div>
IIRC, that was in reference to version 3.3.1, which turned out to be the result of a broken Ubuntu package, and was not a problem with Gromacs itself.<br>
<br>
Try it in the context of the actual molecule, if topology construction requires the next residue. In isolation, that residue will always fail with +N.<br>
<br>
-Justin<br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div class="im">
Thanks,<br>
<br>
Ilya<br>
<br>
<br>
<br>
<br>
-- <br>
Ilya Chorny Ph.D.<br>
<br>
<br></div>
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</blockquote>
<br>
-- <br>
========================================<br>
<br>
Justin A. Lemkul<br>
Graduate Research Assistant<br>
ICTAS Doctoral Scholar<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>
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</blockquote></div><br><br clear="all"><br>-- <br>Ilya Chorny Ph.D.<br><br>