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On 26/03/2012 4:13 PM, Jackson Chief wrote:
<blockquote
cite="mid:CABX=Nyesc3eFn5D9sxMMtY6c5QrMfkNDGi++5-oC0JhFDB6wPg@mail.gmail.com"
type="cite">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.</blockquote>
<br>
The bonds you see are guessed by VMD from the coordinates. They have
only fortuitous correlation with your system topology as constructed
by pdb2gmx... which brings us back to you describing how you are
treating the gap.<br>
<br>
The MD is apparently bringing the two "termini" close together,
which is likely in response to a bonded interaction between them
that you set up with your usage of pdb2gmx. If so, then it will have
issued a warning about it...<br>
<br>
Mark<br>
<br>
<blockquote
cite="mid:CABX=Nyesc3eFn5D9sxMMtY6c5QrMfkNDGi++5-oC0JhFDB6wPg@mail.gmail.com"
type="cite">
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<div class="gmail_quote">On Sun, Mar 25, 2012 at 9:48 PM, Mark
Abraham <span dir="ltr"><<a moz-do-not-send="true"
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>
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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>
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.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>
-- <br>
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