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forlilab / Meeko

Interfacing RDKit and AutoDock
GNU Lesser General Public License v2.1
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Reactive Docking - *.maps.fld is not generated and does not exist #79

Closed guzh970630 closed 2 months ago

guzh970630 commented 10 months ago

Hello, I'm a doctoral student. I ran the Auto-gpu, but there was a problem. "Error: Can't open fld file .maps.fld. Error: get_gridinfo failed with fld file specified with parameter at _config:2." I found that there is no .maps.fld in generated files through mk_prepare_rector.py. Currently, the generated receptor files are: .reactive_config, _flex.pdbqt, _rigid.gpf, _rigid.gpf.pdb and _rigid.pdbqt. I want to konw how to generate *.maps.fld. Thanks

diogomart commented 10 months ago

Hello, see autogrid instructions here: https://autodock-vina.readthedocs.io/en/latest/docking_basic.html#optional-generating-affinity-maps-for-autodock-ff

guzh970630 commented 10 months ago

Hello， I'm sorry. I still haven't solved my problem. The article I refer to is "Reactive Docking: A Computational Method for High-Throughput Virtual Screenings of Reactive Species" I want to perform the “Reactive Docking”. I have completed the first four steps in Reactive Docking. I've got the files .reactive_config, _flex.pdbqt, _rigid.gpf, _rigid.gpf.pdb, rigid.pdbqt and .pdbqt. I'm going to the "Configure AD-GPU for reactive docking". Then I followed the prompt on github "ADGPU -I .reactive_config -L sufex1.pdbqt -N sufex1_docked -F *_flex.pdbqt -C 1"

Found "Error: Can't open fld file .maps.fld. Error: get_gridinfo failed with fld file specified with parameter at _config:2."

Because there is no file input about ".maps.fld" in the command, and ".maps.fld" is not generated before. Can you tell me why I get an error when I run Autodock-gpu with this command, and how I should change the command to make Autodock-gpu run successfully? In addition, I can follow the tutorial you gave me to generate "*.maps.fld", but how to generate "-l .glg" needed to generate ".maps.fld"?

Last, I want to ask you, mk_prepare_receptor.py “--box_center_on_reactive_res” is the reactive residue as the box center, do not need to give additional parameters？

diogomart commented 10 months ago

The .gpf file is the input for autogrid, and the .glg is written by autogrid to log information. The maps, consisting of .map files for each atom type, for electrostatics, and for desolvation, as well as the .fld file, are all written by autogrid. See https://github.com/forlilab/Meeko#3-run-autogrid (I think this is what you are following).

You can get autogrid here: https://autodock.scripps.edu/download-autodock4/

mk_prepare_receptor.py “--box_center_on_reactive_res” is the reactive residue as the box center

yes, this places the box center near the sidechain

diogomart commented 9 months ago

I don't understand.

guzh970630 commented 9 months ago

Thank you very much for your patience. I want to ask a question about the force field of Reactive Docking. In which *.py file is the code for the relevant formulas and parameters of the force field required in the process of Reactive Docking？

diogomart commented 9 months ago

https://github.com/forlilab/Meeko/blob/0badd5b04b5f749f0941f83ce08cdbc206dcd665/scripts/mk_prepare_receptor.py#L133-L136

Note that v0.6.0-alpha broke reactive docking preparation, v0.5.0 should be used for reactive docking instead.