[gmx-users] Secondary structure after InflateGRO step - protein in lipid membrane

Justin Lemkul jalemkul at vt.edu
Wed Oct 10 16:26:22 CEST 2012

On 10/10/12 5:43 AM, Shima Arasteh wrote:
>   Hi,
> I'm doing the protein insertion into the lipid membrane. After shrinking for 30 times, I visualized the system, but the secondary structure of protein is still incomplete . How come? I finished the InflateGRO step.

Visualization oddities like these are a result of (1) distorted geometry of the 
protein or (2) atomic overlap with other molecules that cause rendering 
algorithms to fail.  It should be very easy to identify what is going on based 
on the magnitude of forces in EM and visual inspection of the areas with 
"broken" secondary structure.



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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