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

[Shima Arasteh]

I visualized the last output mdrun of KALP15-DPPC simulation, the secondary structure of protein is complete and it seems OK. Can I trust on it and not care about the visualization of system after inflategro?




 
Sincerely,
Shima


----- Original Message -----
From: Shima Arasteh <shima_arasteh2001 at yahoo.com>
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Cc: 
Sent: Thursday, October 11, 2012 12:36 PM
Subject: Re: [gmx-users] Secondary structure after InflateGRO step - protein in lipid membrane



Thanks for your explanation.

I'm doing protein insertion in lipid-membrane following Justin's tutorial steps, but My Protein and Lipid Membrane are different of KALP15 and DPPC. 

Now, when I visualized .gro file of last iteration in KALP15-DPPC ( the simulation what I did sometime ago to learn how protein insertion is ) I see the same problem here too. 
To use the position restrains, I added "define=-DSTRONG_POSRES" to the energy minimization .mdp file and then went through the iteration step.


Sincerely,
Shima


----- Original Message -----
From: Christopher Neale <chris.neale at mail.utoronto.ca>
To: "gmx-users at gromacs.org" <gmx-users at gromacs.org>
Cc: 
Sent: Wednesday, October 10, 2012 7:56 PM
Subject: [gmx-users] Secondary structure after InflateGRO step - protein in lipid membrane

Can you compute the Ca RMSD to the starting structure (using structural fitting) as a function of inflategro step 
and post it somewhere online and link it here? It is very difficult to know what is going on based simply on the 
fact that VMD doesn't render your protein as you expect it to.

Also, did you really follow that tutorial *exactly*, or did you substitute your own protein molecule. If you used
a different protein, I suggest that you go back and redo the tutorial with KALP15 and see if you have the
same problems. 

My guess is that you are not actually using position restraints, despite the fact that you intend to. To check this,
you can do a simulation of your protein in vacuum with and without position restraints and see if you are actually
getting a very low Ca RMSD when using position restraints. Note that the #ifdef statement in your .itp
file must match the define = -D statement in your .mdp file.

I don't know why you would need to go through more inflategro runs to get a proper protein structure.
Inflategro is designed to avoid perturbing your protein while it moves the lipids around.

Chris.

-- original message --


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.


Sincerely,
Shima


----- Original Message -----
From: Christopher Neale <chris.neale at mail.utoronto.ca>
To: "gmx-users at gromacs.org" <gmx-users at gromacs.org>
Cc: 
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.

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

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