search

GHeinzelmann / BAT.py

The Binding Affinity Tool (BAT.py) is a fully automated tool for absolute binding free energy calculations on protein-ligand systems, compatible with the AMBER and OpenMM simulation packages.
MIT License
166 stars 45 forks source link

suggestion: remove CONECT lines from protonated ligand files #36

Closed camattelaer closed 3 months ago

camattelaer commented 3 months ago

Hi

I have encountered the same issue as previously posted (eg #31 and #30 amongst others).

LEaP fails because the aromatic carbons are identified in the mol2 as c3 atoms (aliphatic). This happens due to incorrect CONECT lines in the protonated lig-h.pdb:

...
CONECT    7    5    8    8                                            
CONECT    8    1    7    7    9                                       
CONECT    9    8   10   10   14                                       
**CONECT   10    9    9   11   21**                                       
CONECT   11   10   12   12   22                                       
CONECT   12   11   11   13   23                                       
CONECT   13   12   14   14   24                                       
CONECT   14    9   13   13   25                                       
CONECT   15    1   16   26                 
...

I have in general had better experience running antechamber when the protonated pdb consists only of ATOM lines. If i remove all of these CONECTlines and run antechamber manually, C9 has an aromatic atom type of ca.

Kind regards

Charles-Alexandre

GHeinzelmann commented 3 months ago

Hi Charles, and thanks for your interest in the BAT code. The CONECT lines should not be there, since I remove them from the initially protonated ligand. The part of the code that does this is located in line 157 of the BAT/lib/build.py script.

Perhaps you are using an older version of the code? If not, please confirm that the ligand file (lig-h.pdb) that goes into the antechamber command (line 180 of the BAT/lib/build.py script) really has these CONECT lines in the pdb file. Thanks.

camattelaer commented 3 months ago

Hi

Thanks for your reply. I took the BAT 2.2 version from the release page. (i usually do this so i can have a quick local download and this is usually the 'stable' release)

It is indeed missing the for-loop which gathers the ATOM or HETATM records. I simply did the same thing yesterday (although via a subprocess call to sed) and it enabled to run the 2.2 version.

Closing this issue since it has already been implemented in the newer version.

Thank you for your time and kind regards!

CA