The missing residues correspond to a loop that connects two alpha helices. The C-terminal end of one helix, and N-terminal end of the other helix contain a random coil. After energy minimization, the coils are extended in space and not connected. I visualized this by looking at the .gro file in VMD. After 5ns of unrestrained MD, the two coils are clearly connected by looking at the output .gro file in VMD. Weird.<div>
<div><br></div><div><br><br><div class="gmail_quote">On Sun, Mar 25, 2012 at 9:48 PM, Mark Abraham <span dir="ltr"><<a href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</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">On 26/03/2012 12:20 PM, Jackson Chief wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
I made a model of a receptor protein, bilayer, and solvent. My protein contains a 20 residue gap. This gap corresponds to a region of the protein that had been digested by trypsin before crystallization. The trypsin digestion has no affect on receptor activity experimentally. I performed energy minimization without problem. The protein looked like it should, containing the gap.<br>
</blockquote>
<br></div>
You have to treat this gap somehow. Either you have to cap the peptide chains (see pdb2gmx -h), or model in the missing residues using some (non-GROMACS) software.<div class="im"><br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<br>
When I performed equilibration, the output had the C-terminus of one protein fragment connected to the N-terminus of the other protein fragment. I don't know how this peptide bond was created, because it was not in the input *.gro file to grompp. Please help.<br>
<br>
</blockquote>
<br></div>
.gro files have coordinates, never bonds. Since you haven't described how you are treating the gap, and haven't said how you've observed the "creation" of a peptide bond, it's hard to give specific guidance.<span class="HOEnZb"><font color="#888888"><br>
<br>
Mark<br>
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</font></span></blockquote></div><br></div></div>