Dear experts,
Im trying to do docking study using autodock4.
Being a newcomer to this field, i face difficulty in rectifying the errors.
Kindly help me to sort this error in the attached log file.
Dear madam,
error message (autogrid4: ERROR: can't find or open receptor PDBQT file "1e7u.pdbqt")
I think you getting error to run the Autogrid program. You have to save your pdbqt files properly to overcome this issue. In Autodock4, the PDBQT files are used store the atomic coordinates, partial charges and AutoDock atom types for both the receptor and the ligand. ( I 'm also a beginner for autodock4)
You have to save your ligand as .pdbqt first after identification of Torsion.
Then in the grid box setting steps, You have to choose the macromolecule (protein) and save it as .pdbqt file format.
While you complete these steps carefully you can run the Autogrid program.
Hope it give some idea to solve this issue
Hi Lakshmi.
From "autogrid4: ERROR: can't find or open receptor PDBQT file "1e7u.pdbqt"." Possible reasons could be
1. 1e7u.pdbqt is not in the path location
2. The pdb is not properly converted to PDBQT
3. Your working directory labelling might be wrong.
Dear dhadapani arumugam,
Thanks for your suggestion. could you help me to get IR, NMR and theoretical crystal sudies of metal complex as you did for cpl paer. i will give the authorship.if it is ok give your maild id. i will contact you.
Dear thirumal kumar,
Thank you for your answer. i will come back to you if i face any difficulty.
Dear thirumal kumar,
Now the error in autodock read like this. could you help me to fix this issue.
autogrid4: ERROR: Grid data file needs the extension ".fld" for AVS input
Dear madam,
I feel glad to work with you. Thank you.......
e-mail: [email protected]
Dear dhandapani
Thank you for accepting collaboration. we will start the work soon
Dear Lakshmi
Make sure that pdbqt file name is without space. This is due to improper GPF file. I suggest you have look on https://www.youtube.com/watch?v=awGrWBEk8Q0 for beginners
Did you find a solution for that error autogrid4: ERROR: Grid data file needs the extension ".fld" for AVS input
I have the same problem what should i do ?
Ph_Noha Gamal, perhaps you have not prepared your .gpf file properly. Repeat the procedure for .gpf file format your error would get rectified; if not then, see this attachment pg. 17 to pg. 21; this might be of some help.
Ph_Noha Gamal please remove any space in your input file names. fld will resolve. check.
All the best
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