Dear AMBER users,
I am trying to run MMPBSA script on 10 ns simulation trajectory.( My protein-ligand complex system has 579 residues. It is a multidomain protein; active domain and regulatory domain are situated far away from each other, but linked by a large loop. Ligand is present in an active domain). Extraction of coordinates is done successfully but during binding energy calculation job gets aborted at first coordinate only with the error "complex_vac.prmtop not successful".I have tried the adjustment with fillratio (2,3 or 4) but it didn't help. Waiting for suggestions
Thank you.Jyotsna
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Received on Mon May 07 2012 - 00:00:03 PDT
