Dear AMBER users,
I am trying to understand the folder details of Advanced thermodynamic
integration calculation (Link:
https://ambermd.org/tutorials/advanced/tutorial39/index.php). initial/
folder is having frcmod, lib,mol2 and pdb files for 2 systems (1h1q~1h1r).
In case of rbfe, did FE_workflow create the 1h1q~1h1r transformation
folder under CDK2 ? And, transformation folder has aq and com folders
respectively. In case of aq folder, is "stateA.rst7" belongs to ligand A ?
Then how to get .rst7 for ligand B ? I mean rst7 for another end state is
missing. Also, is "unisc.parm7" file belong to merged topology file i.e,
for two ligands ?
In case of com folder, I find "stateA.rst7" and "stateB.rst7" files that
means for two end states is present. Why aq and com has different rst7
formalism ?
And, /rbfe/CDK2/1h1q~1h1r/aq/inputs/ has 23 input files fro each lambda
windows. Whatever I understood, 21 different stages performed before TI.
Why this is so ? Kindly clarify.
Your suggestions would be appreciated.
Thanks & Regards
Kankana Bhattacharjee
Ph.D. Scholar
Department of Chemistry
Ashoka University
Sonipat, Haryana
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Received on Tue May 28 2024 - 00:00:02 PDT
