Dear Amber users,
I recently re-compiled AT15 and amber11, then realized the mmpbsa.py is upgraded. However, I cannot figure out how to use the receptor mask. For example, in this command:
ante-MMPBSA.py -p apt2loop13_solvated.prmtop -c apt2loop13_solvated.inpcrd -cp complex.prmtop -rp receptor.prmtop -lp ligand.prmtop -strip_mask ":WAT:Na+" -receptor_mask ":.1-5099"
The receptor should include atoms 1 to 5099, but it didn't work. What should be the right mask? I am looking forward to your help.
Thank you very much.
Best,
Bin
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Received on Mon Nov 21 2011 - 19:00:04 PST
