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

[Christopher Neale]

What, precisely, do you mean the SS of the protein is still incomplete? When you use inflategro, the conformation of your 
protein is intended to remain as in your initial conformation. Did you forget to use position restraints
on your protein during the contraction steps ( http://www.csb.bit.uni-bonn.de/inflategro.html )?

If it is just a visualization artefact, then you should be able to select only the protein in VMD and it 
should display just fine.

Chris.

-- original message --

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.

Thanks for your suggestions in advance.

Sincerely,
Shima