[gmx-users] grompp is adding a bond in my model that should not be there

Mark Abraham Mark.Abraham at anu.edu.au
Mon Mar 26 08:36:09 CEST 2012

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 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.

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.

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...


> On Sun, Mar 25, 2012 at 9:48 PM, Mark Abraham <Mark.Abraham at anu.edu.au 
> <mailto:Mark.Abraham at anu.edu.au>> wrote:
>     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 receptor activity experimentally. I performed energy
>         minimization without problem.  The protein looked like it
>         should, containing the gap.
>     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.
>         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.
>     .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.
>     Mark
>     -- 
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