Hi,
To simulate lipids in AMBER using the Charm36 lipid force field you need to use force-switching, as the paper specifies. This is only available in Amber16. I think this is particularly important for DPPC, possibly less so for other lipid types but don't quote me on that.
I've run GPCR simulations with Lipid14 (POPC lipid), I'd suggest doing your own validation of this set up.
All the best,
Callum
________________________________
From: Shanghaitech University WuMeng <wumeng.shanghaitech.edu.cn>
Sent: Thursday, February 9, 2017 8:08:38 AM
To: amber
Subject: [AMBER] CHARMM36 force field
Dear All,
I am working on a membrane protein(GPCR) simulation with Amber. I have researched some literature before and found that the charmm force field such as CHARMM36 force field was commonly used in the membrane protein MD simulations. I have read this paper
http://pubs.acs.org/doi/abs/10.1021/acs.jctc.5b00935 , in this paper it said "the use of the C36 lipid FF in AMBER (versions 14 and earlier) may not agree with CHARMM/NAMD to the degree obtained with programs that contain the force-based switching function for the LJ potential". The Amber version in our lab is 14 exactly, so what should I do if I want to apply CHARMM36 force field to my simulation. Actually I am not sure if the charmm force field is necessary for membrane protein MD simulation or not, maybe the lipid14 force field is also OK! Any suggestions would be greatly appreciated.Thank You Very Much!
Sincerely,
Wu Meng
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Received on Fri Feb 10 2017 - 09:00:03 PST
