Hi Ning,
Yes, Lipid14 would be a better choice because Lipid11 and GAFFlipid are deprecated. We now recommend Lipid14 for lipid simulations. POPG was only available with the Lipid11 force field. The lipid14_supp.lib file contains the old Lipid11 residues that were not updated in Lipid14 at the time of publication last year. So lipid14_supp.lib should not be used unless you are doing your own parameterization work for those residues.
With that being said, Callum Dickson refined some of the parameters for the PG head group and I am preparing a manuscript that includes the new parameters. If you contact Ross Walker and I off the mailing list we can discuss trying out the new parameter set.
Best,
Ben Madej
San Diego Supercomputer Center
________________________________________
From: Ning Xiang [xiangn.purdue.edu]
Sent: Friday, June 26, 2015 7:16 AM
To: amber.ambermd.org
Subject: [AMBER] Lipid 14 force field
Hi,
Currently, I am running some lipid simulation using Amber force field. Since our simulation is using mixed membrane which is hard to find a good surface tension with Lipid11, so Lipid14 with NPT would be a better choice. However, one of the component we used is POPG lipid. We can find the PGR residue in the lipid14_supp.lib in Amber14 release, but LJ parameters for some atom types (e.g., Oh,hO) are missing. I am wondering if it is reasonable now to use residues in lipid14_supp.lib. Could you please advise? Thank you very much.
Best regards,
Ning Xiang
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Received on Fri Jun 26 2015 - 11:00:03 PDT
