Hi, everyone ! I try to extract the docking pose from a silent file which contains the ligand docking results. Here is my code:
extract_pdbs.mpi.linuxgccrelease -in:file:silent job01.o -in:file:tags BLS_0092 -extra_res_fa BLS.params -in::file::fullatom -database main/database
and the followings are output warning info:
Number of atoms in pose and silent file disagree! Attempting to continue ...
(in residue PRO:NtermProteinFull at 1 natoms_pose=18atm_seqpos 1 natoms_struct=17)
Likely explanations:
1. You are trying to extract, with residue type set A, a silent file created with residue type set B.
2. The database has been updated since your silent file was made, meaning the definition of this RT has drifted.
3. You have passed an argument to -database that indicates a database out of sync with your chosen executable.
Then I checked the output pdb in pymol, and found that the protein and the ligand are far away from each other, but the cofactor and the ligand seems in the right place. It is very strange and I make sure the docking input files are ok because I used the same parameters except setting the output file as pdb format and the result was normal.
I'm not quite understand what's the meaning of the first explanation, but the database has not been changed.
Any suggestions would be greatly appreciated, thank you !
Ruska
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