[gmx-users] Tryptophan rings are not connected in visualization

[Justin Lemkul]

On 5/17/13 10:08 PM, Shima Arasteh wrote:
>
> Hi,
> I am simulating a system composed if POPC , peptide, waters and ions.
> I used the InflateGRO methodology to construct the system.
> There
>   are 2 Tryptophan residues in my peptide. Each Tryptophan has 2rings
> connected from one side. After inflategro one of the Tryptophan rings is
> normal, but the other is not because  What I see them in vmd, there are
> 2rings remain close to eachother but the expected bonds between them are
>   not visible.
> The top file shows the correct bonds and angles and ... .
> I ran EM, NVT, NPT, and thought this problem would be solved but it is still as well as before.
> The EM was also ok and did not show high enegy or crash.
> Does this problem relate to the vmd and its algorithms? Or there is a problem with my system.

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

The topology is definitive.  VMD is not.

> How would the rings look usual? How could I solve it?
>

Run EM.  InflateGRO should not have messed with the coordinates though.  If the 
bad geometry is a result of EM, that means you have really nasty forces 
somewhere in the system.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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