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

Shima Arasteh shima_arasteh2001 at yahoo.com
Wed Oct 10 18:06:13 CEST 2012

I exactly followed the steps in Justin's tutorial of KALP15-DPPC, so I applied position restrain to restrain the protein in the step before iteration.

It doesn't seem to be artifact, because when I select only the protein in VMD, I see a broken secondary structure.
Sometime ago, other gmx users suggested that when one is using inflategro, it's not expected the complete secondary structure and it's needed to go through the iteration. I did iteration but it's still as before.


----- Original Message -----
From: Christopher Neale <chris.neale at mail.utoronto.ca>
To: "gmx-users at gromacs.org" <gmx-users at gromacs.org>
Sent: Wednesday, October 10, 2012 7:09 PM
Subject: [gmx-users] Secondary structure after InflateGRO step - protein in lipid membrane

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.


-- 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.


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