Date: Mon Apr 23 2012 - 17:46:17 CDT
There is a very old post in the list asking this question just around the time when the alchemify program was no longer needed to run FEP simulations. So, as far as i understand if i write an amber topology including both of my states in the same file and then i create the pdb with the definitions of both end states then NAMD will be able to infer the exclusion list even when you ask it to read the exclusion list from the prmtop file (as required for the AMBER files).
Has anybody tried this? Or do any of you know if this approach works?
The other chance is to use one of this CHARMM formatted amber residue topology files, but i'd rather use the files created by AmberTools itself.
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