[gmx-users] Membrane protein tutorial

[Stephane Abel]

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> Today's Topics:
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>    1. RE: g_sdf (Dallas B. Warren)
>    2. Membrane protein tutorial (Justin A. Lemkul)
>    3. distance restraints in Gromacs 4.0.4 (Ivan Gladich)
>    4. Pressure Coupling Problem (Joe Joe)
>    5. Pressure Coupling Problem (chris.neale at utoronto.ca)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Wed, 08 Apr 2009 09:41:44 +1000
> From: "Dallas B. Warren" <Dallas.Warren at pharm.monash.edu.au>
> Subject: RE: [gmx-users] g_sdf
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
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> 	<89907EA1DCFB7548A431C13A270F9DD50701997B at prk-exch-01.vcp.local>
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> What exactly your issue with using g_sdf?
>
> You need to supple a trajectory, index, and topology.  Index contains
> the three reference atoms for the molecule, plus the atom you are
> calculating the sdf to.  Selection of the correct grid size and binwidth
> is required to get something that looks as you want it.
>
> Catch ya,
>
> Dr. Dallas Warren
> Department of Pharmaceutical Biology and Pharmacology
> Pharmacy and Pharmaceutical Sciences, Monash University
> 381 Royal Parade, Parkville VIC 3010
> dallas.warren at pharm.monash.edu.au
> +61 3 9903 9167
> ---------------------------------
> When the only tool you own is a hammer, every problem begins to resemble
> a nail. 
>
>
> ------------------------------
>
> Message: 2
> Date: Tue, 07 Apr 2009 19:55:28 -0400
> From: "Justin A. Lemkul" <jalemkul at vt.edu>
> Subject: [gmx-users] Membrane protein tutorial
> To: "Gromacs Users' List" <gmx-users at gromacs.org>
> Message-ID: <49DBE7F0.4040804 at vt.edu>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
>
> Hello all,
>
> Due to the recent influx in questions related to membrane proteins (especially 
> with common questions), I decided to put together a step-by-step tutorial for 
> membrane protein systems.  It's a work in progress, so I would genuinely 
> appreciate feedback from anyone who has a few minutes to take a look.  These 
> procedures make sense in my head, so hopefully that comes through in the 
> instructions :)
>
> I have posted a link on the wiki site to my tutorial:
>
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/index.html
>
> I hope that people find this useful.  I have attempted to walk the user through 
> most practical concerns that arise regarding topology organization and a few 
> analysis questions that show up on the list frequently (g_order, g_density, etc).
>
> If you have comments or questions, please do not hesitate to send me a private 
> message.
>
> -Justin
>   
Thanks Justin for this effort, This is a great job.

Stefane