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.
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
Subject: namd-l: parameter file for DMPC lipid and protein system but with
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.
-- Dr Erica Smith Lecturer in Chemistry School of Science and Technology University of New England Armidale NSW 2351 Australia Phone 61 2 6773 5130 Facsimile 61 2 6773 3268 Mobile 0488 167 589 Email erica.smith_at_une.edu.au http://www.une.edu.au/study/chemistry/ http://blog.une.edu.au/Chemistry/ CRICOS Provider Code 00003G
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