Hello,
I am trying to run a SPE calculation using the FF's in the Amber suite.
I am using the Packmol-Memgen tool within AmberTools to generate a membrane bi-layer, then I edit it by maintaining a single leaflet to get a structure of a single layer patch of a membrane (in my case I use a homomembrane of POPC lipids, which should be simple since the POPC lipid isn't charged and hence shouldn't be neutralized by ions at the Packmol-memgen step). When I try to run pdb4amber I get an error that indicates that the naming of the lipids isn't consistent with the naming within Amber, so it crushes, and I don't even get to the step of generating the coordinates and topology files using tleap to then run on Amber.
It should be noted that when I tried to run a SPE calculation on a single POPC lipid it worked, and I got a normal termination and an output file.
I am running Amber on a PBS server account, and I am using Amber24 and AmberTools24. It also should be noted that I use Gaussview as my molecular editor and I save the files in a pdb format (maybe this is also an issue, if so, what other software do you recommend?). I have some questions, and I am seeking any help since I am lost.
1. How can I fix my system pdb files so they will successfully go through pdb4amber?
2. Do you have any example input pdb files I can look at and maybe make a script to copy the format?
3. If I want to add a small peptide on top of the single layer patch membrane (to mimic an adsorption initial conformation) and calculate the interaction energy using an SPE as mentioned before, how would you recommend doing it?
4. Are there any logical flaws in my workflow that are popping out to you that you think I should change?
Thank you very much for your attention and support,
Benji
M.E student at the Dana Research Group, Technion
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Received on Sat Jan 04 2025 - 11:00:02 PST
