Dear All,
{Sorry for long mail}
As lipids are hot now these days on AMBER archive, I was trying to do some simulations on DMPC, which still I think not there in AT12 (that charmmlipid2amber.x supports conversion). So instead I tried using DMPC gaff params by Gould et al.'s J. Comput. Chem. Vol 29, page 24-37. But I have some doubts:
1) The atom type used for Phosphorous is p4 (gaff), which is actually should be p5. To recall the things, p4 type is for P attached to three atoms, while p5 is used for P with four atoms. What can be the reason?, I wonder to choose p4 as I see there is much difference in the bond, angles and torsional terms though compared to p5, vdw remains same.
2) Secondly the paper uses and validate many things with "S" configuration DMPC bilayer (the single residue is in "S" configuration, as provided in Richard's Bryce website). So can I assume these validations remain same for "R" configurations as DMPC lipid is R (I dont have reference for that though, but what CHARMM-GUI provides and other lipids are in R form only.). So is there any special reason 'S' lipid was used in such study? Anyhow I can use params for R also.
3) Few lipids are there now in lipid11 (that charmmlipid2amber.x uses). As far I was following recent archive mails AMBER will provide params which can be used without surface tension once it is published. So the params in lipid11 will change after it is published or these are same params which can be used without surface tension?
regards,
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Received on Fri Jul 13 2012 - 02:00:02 PDT
