Dear Amber users,
I installed MMPBSA successfully, then calculated the binding energy of a
protein-DNA system without any problem. Now I am trying an antigen-antibody
system, but got this error massage:
ptraj found! Using /usr/local/amber10/exe/ptraj
sander found! Using /usr/local/amber10/exe/sander
Assuming /usr/local/amber10/exe/sander is part of
amber9 or amber10. Using old PB input file.
Warning: igb=2 should be used with mbondi2 pbradii set. Yours are modified Bondi
radii (mbondi)
Preparing trajectories with ptraj...
Error! Ptraj failed. Check coordinate and topology files for the complex.
NOTE: All files have been retained for debugging purposes. Type MMPBSA.py
--clean to erase these files.
I tried to add mask for the receptor and ligand:
receptor_mask=':530-1435', ligand_mask=':1-529',
But still got the same error.
What should I do to figure out the problem? Thank you very much.
Bin
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Received on Wed Nov 24 2010 - 09:30:04 PST
