AutoDock-Vina
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ccsb-scripps
AutoDock Vina
https://github.com/ccsb-scripps/AutoDock-Vina/blob/d13f9e93e253573b01ffbb28cfd1e2dd26ff9002/docs/source/docking_hydrated.rst?plain=1#L138 When I use Vina forcefield, I get this error: `ERROR: Affinity map for atom type C_H is not present`. How to fix this problem?
Seems like when the batch input mode is specified from the config file, vina (as installed from conda, AutoDock Vina 58016d8-mod) does not recognize the batch option and tries to...
An internal error occurred in D:\a\AutoDock-Vina\AutoDock-Vina\src\lib\tree.h(101). I have run batch process script in python with glob module, but instead of going in serial it is skipping, like 0, then it...
I already have computed the ligand center according to the input ligand.pdbqt, then I use the following script to calculate the vina.score( ) ： ``` v = Vina(sf_name='vina') rec_file =...
When I use ADFR to process pocket.pdb of PDBbind dataset, there are four pocket files fail to be processed: ``` 3ijh_mutate2_pocket:B:ALA100C:C and 3ijh_mutate2_pocket:B:ALA100C:C have the same coordinates Traceback (most recent...
I heard that there is some sf than can be used in metal ions(Mg,Se,Zn...) docking in AutoDock Vina, But I couldn't find it in manual. Is there anything to do...
:thought_balloon: I find that an include guard like “[`VINA_H`](https://github.com/ccsb-scripps/AutoDock-Vina/blob/d13f9e93e253573b01ffbb28cfd1e2dd26ff9002/src/lib/vina.h#L23 "Update candidate")” is too short for the safe reuse of your header file (when it belongs to an application programming interface).
I have just run a docking simulation using the hydrated Vina protocol [(link to protocol)](https://autodock-vina.readthedocs.io/en/latest/docking_hydrated.html) for the first time. In the next step, I want to calculate the RMSD between...
This tells the build to check the standard Linux locations for the ARM64 boost libraries. It builds for ARM64 without issues once it locates them.
