[AMBER] MMPBSA - calculating energy decomposition by residue in a trajectory without a ligand

From: <Andrew.Warden.csiro.au>
Date: Wed, 18 Jun 2014 21:53:57 +0000


I am running into problems with the apparent requirement for a ligand.prmtop, complex.prmtop, solvated.prmtop in MMPBSA.py when I just want to calculate the energy contribution per residue over an MD trajectory. Is there some way around this? For reference, I want to simply run:

Input file
   startframe=1000, endframe=2000, interval=50,
   verbose=2, keep_files=0,
   igb=5, saltcon=0.1,
   idecomp=1, print_res='1-1456',

Many thanks for your help.


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Received on Wed Jun 18 2014 - 15:00:02 PDT
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