when performming an alanine scanning calculation on the binding free energy , I got a error.
error message:
Loading and checking parameter files for compatibility...
mmpbsa_py_energy found! Using /home/mmpbsa_py_energy
cpptraj found! Using /home/cpptraj
Preparing trajectories for simulation...
Error during FileIO_Std::Read: Input/output error
Error during FileIO_Std::Read: Input/output error
Mutating trajectories...
MutateError: Mismatch in atom # in residue VAL. (16 in alamdcrd.py and 27 passed in)
Exiting. All files have been retained.
commands that I used to create mutant promtop files:
(tleap)
source leaprc.ff03ua
com_mut = loadpdb complex_mutant_val115.pdb
re_mut = loadpdb receptor_mutant_val115.pdb
saveamberparm com_mut complex_mutant_val115.prmtop complex_mutant_val115.inpcrd
saveamberparm re_mut receptor_val115.prmtop receptor_val115.inpcrd
quit
MD file: https://drive.google.com/folderview?id=0B6PKsnnnVbH1M0tiQmV1Ymk1bU0&usp=sharing
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Received on Wed Mar 12 2014 - 05:00:03 PDT
