[gmx-users] structural clashes make the structure look like broken?

[Dallas Warren]

From
http://www.gromacs.org/Downloads/Related_Software/Visualization_Software#Topology_bonds_vs_Rendered_bonds

"Remember that each of these visualization tools is only looking at
the coordinate
file <http://www.gromacs.org/Documentation/File_Formats/Coordinate_File>
you gave it (except when you give gmx view a .tpr file
<http://www.gromacs.org/Documentation/File_Formats/Topology_(.tpr)_File>).
Thus it's not using your topology
<http://www.gromacs.org/Documentation/File_Formats/Topology_File> which is
described in either your .top file
<http://www.gromacs.org/Documentation/File_Formats/.top_File> or your .tpr
file
<http://www.gromacs.org/Documentation/File_Formats/Topology_(.tpr)_File>.
Each of these programs makes their own *guesses* about where the chemical
bonds are for rendering purposes, so do not be surprised if the heuristics
do not always match your topology. Apply your brain, here!"

Catch ya,

Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.warren at monash.edu
---------------------------------
When the only tool you own is a hammer, every problem begins to resemble a
nail.


On Fri, 2 Aug 2019 at 18:16, sunyeping <sunyeping at aliyun.com> wrote:

> Dear all,
>
> I am doing MD of a protein-DNA complex. There are some structural clashes
> between the DNA and the protein, but both of them look complete (Please see
> the figure at
> https://drive.google.com/file/d/1K7xiv4Lf7UEggNIykWxXX2WRtclJxv2q/view?usp=sharing.
> The clashes are indicated by the red arrows). However, after I prepared the
> gro file with pdb2gmx, did energy minimization, when I did nvt and npt
> equilibrium, I found that one of the  DNA chain became broken (Please see
> the figure at
> https://drive.google.com/file/d/1FtGPWjhnEqbWchmQaWEA3YpSqWca5Eyd/view?usp=sharing.
> The broken site of the DNA is indicated by the red circle).
>
> I think the break in the DNA is caused by the structural clash between the
> DNA and the protein and the clashing atoms can not be shown in the
> visulization software (such as pymol and vmd).
>
> I am wondering whether the structural clashes will finally disappear in a
> prolonged simulation or it will kept. If the MD simulation will not remove
> the structural clashes, I should give up it. What do you think? Do you have
> any idea of removing the structural clashes in the initial structure?
>
> Best regards.
> --
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