On 26/03/2012 4:13 PM, Jackson Chief wrote:
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 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
On 26/03/2012 12:20 PM, Jackson Chief wrote:
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
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
Hey,
The problem is likely that pdb2gmx created the bond. It will have given a
long bond warning. You can add a ter statement in the pdb file at the break.
Cheers,
Tsjerk
On Mar 26, 2012 5:49 AM, Mark Abraham mark.abra...@anu.edu.au wrote:
On 26/03/2012 12:20 PM, Jackson Chief wrote: I made
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