Hello,
I am attempting to run a MD simulation of a GPCR with G-protein heterotrimer attached. The receptor itself is embedded in a lipid membrane (POPC:CHL1 9:1; following the callumjd (
https://github.com/callumjd/AMBER-Membrane_protein_tutorial) example on the amber website for building a membrane). Three of the residues on this membrane are lipidated so a N-myristoylated glycine, S-palmitoyl cysteine, and S-geranylgeranyl cysteine (built using this tutorial
https://carlosramosg.com/amber-custom-residue-parameterization). The lipidated residues are embedded into the membrane so imagine that lipid moiety interacting with the other lipids of the bilayer. I was able to generate the parm7 and ncrst files succesfully. My issue is now with the equilibration phase.
Using the same general workflow as callumjd, I held the protein backbone when initiating ntp=3 and the other parameters used. After I release the restraints, the run ends prematurely. After using the cpptraj "checkstructure" function, the box dimensions continue to change. I attempted to continue to run it multiple times so that it would eventually stop changing and crashing, however, that did not work. I have tried this with ewald of 3 and ewald of 5 but both have not worked. Do you have any ideas as to what I could try next?
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Received on Fri Jul 05 2024 - 08:30:02 PDT
