Hi,
For your molecule, with RED did you try to separate your molecule in two parts : dodecyl and charged phenylalanine ? to see if you obtain the same charges ? More which level of theory you used in your QM calculations ?
>> Could you advise the best force field to use for this head group? Should I use ff99SB and GAFF or something else?
I would suggest you to use AMBER99SB, since your headgroup is the phenylalanine residue.
HTH
Stephane
________________________________________
De : Covington, Cody Lance [cody.l.covington.Vanderbilt.Edu]
Date d'envoi : lundi 15 avril 2013 21:52
À : AMBER Mailing List
Objet : Re: [AMBER] GAFFlipid using custom lipids
Ben
> What type of phospholipid are you interested in parameterizing?
I am actually doing a surfactant that is the dodecyl ester of phenylalanine, so the head is a phenylalanine, with a protonated nitrogen(very different from your lipids).
Could you advise the best force field to use for this head group? Should I use ff99SB and GAFF or something else?
> The GAFFlipid paper explains in detail the way that dihedral scans were compared with QM energies, and goes into depth about the charge derivation approach.
I have tried the REDs server using the entire molecule and a +1 charge, but I gives a net charge on the "tail" of about 0.4 e. I think this is a large charge for a carbon chain, so I was going to use a 2 part charge fitting described in the Lipid11 paper and compare results. Does this sound reasonable?
Thanks
Cody
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Received on Mon Apr 15 2013 - 14:00:02 PDT
