I am getting an error when running the mmpbsa.py script.
I am running the following script.
/usr/local/amber12/bin/MMPBSA.py -O -i pbsa.in -o FINAL_RESULTS_MMPBSA.dat
-sp ../full.prmtop -cp ../complex.prmtop -rp ../receptor.prmtop -lp
../ligand.prmtop -y ../full-equil6.mdcrd ../full-equil7.mdcrd
../full-equil8.mdcrd ../full-equil9.mdcrd ../full-equil10.mdcrd.
I did the same for the previous system but did not get this error. Can
anyone suggest a solution. Thank you.
error msg
mmpbsa_py_energy found! Using /usr/local/amber12/bin/mmpbsa_py_energy
cpptraj found! Using /usr/local/amber12/bin/cpptraj
Preparing trajectories for simulation...
Error: Atom 24576 was assigned a lower molecule # than previous atom.
Error: This can happen if bond information is incorrect or missing.
Error: Detected # of molecules is 90860. If this is incorrect and your
Error: topology does not have bond information (e.g. PDB file), try
Error: increasing the bond search cutoff offset (currently 0.200000).
Error: e.g. 'parm full.prmtop bondsearch <new offset>'
Error: Could not open parm ../full.prmtop
--
Chinthaka Nadun Ratnaweera
Hand Lab Rm 1126
Mississippi State University
310 Presidents Circle
Starkville, MS 39762
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Received on Mon May 06 2013 - 07:30:05 PDT
