From: Prathit Chatterjee (pc20apr_at_yahoo.co.in)
Date: Tue Jan 04 2011 - 01:14:10 CST
Please concatenate the charmm_36 lipid file and the par_all22_prot_cmap.inp to a new *.inp file and use it for the lipid system containing the protein.
Regarding replacement of the charmm27 lipid parameters by the charmm_36 lipid parameters, please go through the paper - J. Phys. Chem. B 2010, 114, 7830–7843. This gives the difference and the development of the recent charmm_36 force field from the previous one (charmm_27).
So, combining the recent force field with the par_all22_prot_cmap.inp will be the correct decision according to me.
--- On Tue, 4/1/11, Erica Smith <esmith32_at_une.edu.au> wrote:
From: Erica Smith <esmith32_at_une.edu.au>
Subject: namd-l: parameter file for DMPC lipid and protein system but with CHARMM36 lipids
Date: Tuesday, 4 January, 2011, 9:23 AM
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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