RE: parameter file for DMPC lipid and protein system but with CHARMM36 lipids

From: JC Gumbart (gumbart_at_ks.uiuc.edu)
Date: Mon Jan 03 2011 - 23:34:18 CST

Best would be to use two separate parameter files for protein and membrane;
NAMD can refer to as many as you want. I believe the CHARMM distribution
already includes them individually.

-----Original Message-----
From: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] On Behalf
Of Erica Smith
Sent: Monday, January 03, 2011 9:54 PM
To: namd-l_at_ks.uiuc.edu
Subject: namd-l: parameter file for DMPC lipid and protein system but with
CHARMM36 lipids

Hello,

Has anyone used the charmm36 lipid parameters to simluate a lipid system
containing a protein? In other words using a parameter file such as
par_all27_prot_lipid.inp but with with charmm36 lipid parameters. My
protein is not embedded in the membrane, but sits the within the solvent
pahse (TIP3P water) just above the polar headgroups.

I have not worked with membrane simulations or NAMD for several years, and
am not sure if it is simply a case of just replacing the charmm27 lipid
parameters in par_all27_prot_lipid.inp with the charmm36 lipid parameters.

Thanks,
Erica Smith

-- 
Dr Erica Smith
Lecturer in Chemistry
School of Science and Technology
University of New England
Armidale NSW 2351 Australia
Phone  61 2 6773 5130
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Email  erica.smith_at_une.edu.au
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