Hi,
I have performed MD simulation of a membrane embedded protein with ligands. I would like to perform FEP ligand alchemical mutation using Schrodinger suite and in particular Desmond software. I am facing an issue in converting the whole system into a readable format for desmond to start the FEP ligand transformation. Searching for a solution to this issue, I have converted my amber topology file into .cms (desmond format) following the instructions on this page: http://ambermd.org/desmond.html
The converted file is correctly loaded in maestro but the lipids in my system are loaded as ligands. My ligand shows partial interaction with lipids, therefore in order to perform significative FEP calculation I need that these lipids are recognized by the software as lipids and not as ligands.
Does anyone know how to solve this issue?
You may also address this question to desmond community following this link:
https://www.deshawresearch.com/resources_desmond.html
Hi Carmine,
I am facing exactly the same problem. Did you manage to convert the lipids to a Desmond-readable format?
Thanks
Hi Raquel,
Yes I have problems in converting lipids from my forcefield (AMBER lipid14) in a readable format for maestro/desmond.
I wrote also to the Schrodinger support but their answer was
"Unfortunately, membrane-containing systems won't work with LigandFEP; this feature is only available to Schrodinger customers using FEP+ with their software."
So, I'm stucked now.
- Badges
- Science topic
- Similar topics
- Biological Science
- Biochemistry
- Biomolecules
- Peptides