[gmx-users] Berger lipid

[Shima Arasteh]

Yes, I know that as studied the Kalp15 tutorial.
Sorry, the last question :) 
:

  DO I need to run pdb2gmx to get the top file of POPC in CHARMM36? Is it ok?  Because I see that POPC.itp is also required for simulation of protein in bilayer.

Again, thanks

 
Sincerely,
Shima


----- Original Message -----
From: Justin A. Lemkul <jalemkul at vt.edu>
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Cc: 
Sent: Friday, June 29, 2012 5:16 AM
Subject: Re: [gmx-users] Berger lipid



On 6/28/12 8:43 PM, Shima Arasteh wrote:
> 
> 
> Yes, I have studied the article by Jeffery B. Klauda and other articles related to C36. And know where the parameters of CHARMM36 were derived.
> 
> By the way, when I search the lipidbook to find the .itp file I can't find it! What about the lipid .itp ? Is it required yet? ( in your tutorial it's written "lipid.itp - Berger lipid parameters" )
> 

You do not need the so-called "lipid.itp" as it is for a completely different force field.  The "Berger lipids" are a united-atom parameter set derived in 1997 from a hybrid of OPLS and Gromos parameters.  They are typically combined with Gromos force fields.

-Justin

-- ========================================

Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================


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