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

Shima Arasteh shima_arasteh2001 at yahoo.com
Sat May 18 04:08:34 CEST 2013

I am simulating a system composed if POPC , peptide, waters and ions.
I used the InflateGRO methodology to construct the system.
 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.
How would the rings look usual? How could I solve it?

Thanks in advance.

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