Xu Youjun

Hi Koes, I did a comparison between vina and smina for score_only and local_only mode. score_only comparison !time externals/vina_v1.2.3.1 --config data/case-1/vina_docking_conf.in --ligand data/tmp8jk71etz_rdk.bestscore.pdbqt --score_only real 0m3.377s user 0m2.330s sys 0m1.047s !time externals/smina.static --config data/case-1/vina_docking_conf.in --ligand data/tmp8jk71etz_rdk.bestscore.pdbqt --score_only real 0m0.116s user 0m0.100s sys 0m0.016s local_only comparison !time externals/vina_v1.2.3.1...

May I have to refer to an example file as --flex argument?

I tried the follow command, smina -r examples/protein.pdbqt --flex examples/ligand0009695.pdbqt --autobox_ligand demo.sdf --no_lig --minimize -o examples/out_lig.pdbqt But the parse_error called "Parse error on line 15 in file "examples/ligand0009695.pdbqt": Unknown or inappropriate tag". here in the file is a tag "ROOT" I guess I may should place the root part of the ligand into the Rigid part in the create_init_model?

Hi, I would like to implement a contrained score after the "--minimized". It just means, some part atom positions are fixed in the minimized process. I read the source code of smina, and found the branch tree would be parsed by the ligand OBmol. So I tried to keep the root position not be updated in each step of bfgs. I just understand this root position with p vector (see the following code ) could move the whole ligand positions. Thus I assign zero to them. But the orientations and torsions are...

Okay, I see. Thank you

Yeah, it works. But I tried different atom types, and it return slightly diffrent energy values. I don't know which type is suitable for representing the property of the exclusion volume.

Hello, When I dock a molecule into the binding site, I just want to add a region with the exclusion volume. A sphere is a center with a radius, where the docking molecule would keep a vdw distance to. I would like to know how could I implement this function? Or any suggestions? Thanks Best,