Hi Amber community,
As described in the Amber manual, and here: https://ambermd.org/AmberModels_lipids.php, many types of lipids can be constructed from combinations of available head groups and acyl chains, in LIPID21.
However, is it possible to run lipid simulations (Amber FF) that are not one of the available combinations? For example, I’d like to be able to run simulations with phosphatidylinositol 4,5-bisphosphate (
https://en.wikipedia.org/wiki/Phosphatidylinositol_4,5-bisphosphate), which sadly can’t be constructed from the available LIPID21 fragments.
Any advice about how one should approach this (or if it is even advisable) would be greatly appreciated.
Thanks,
Derek
Derek M. Shore, Ph.D.
Lecturer of Physiology and Biophysics
Scientific Computing Technology Engineer
Institute for Computational Biomedicine
Weill Cornell Medicine
Department of Physiology and Biophysics
1300 York Avenue, Room LC501A
New York, NY 10065
T: 212-746-6386
des2037.med.cornell.edu<mailto:des2037.med.cornell.edu>
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Received on Thu Mar 14 2024 - 15:30:02 PDT
