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

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.
best

Prathit

--- 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
To: namd-l_at_ks.uiuc.edu
Date: Tuesday, 4 January, 2011, 9:23 AM

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
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