[gmx-users] Secondary structure after InflateGRO step - protein in lipid membrane
jalemkul at vt.edu
Wed Oct 10 16:26:22 CEST 2012
On 10/10/12 5:43 AM, Shima Arasteh wrote:
> 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.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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