/test2/autodock4: I'm sorry; I can't find or open "3POM.SA.map"
Real= 0.47, CPU= 0.47, System= 0.00
While running autodock4 it is showing above error after doing grid run and docking.
Ligand.pdbqt file may probably be corrupted. If it is true, edit the file.
Sure sir ill try to replace with other ligand..and let you know sir,..
Hello.
It seems that a map is missing for atom SA regarding 3POM structure.
You have to recalculate grid map (with Autogrid4) including in the parameter file (*.gpf) the missing atom SA.
Best regards,
Ricardo Ferreira
To add above SA maps using MGL tools GUI follow file preparation protocol till saving Flex and Rigid file of Receptor. After this from Grid tab follow steps mentioned below
1. GRID >> MACRO-MOLECULE >> OPEN >> OPEN YOUR RIGID FILE.
2. SET MAP TYPES >> DIRECTLY >> by default you will find " A C HD N NA OA SA" in text widget and if not then write them manually and ACCEPT.
Follow other part intact and run grid. You can notice the change that after grid log generation you will find a SA.map file in your folder. After this you can perform docking calculation as per your case.
Enjoy.
Dear Gowrishankar,
I think Mr Ricardo is right. Just follow whatever he had said.
Best regards
A valid point from Mr. Ricardo, This error occurs when a certain map is missing in case of a ligand coordinates. for this you can prepare the pdbqt files again and then re run the Autogrid4 to correct this error.
while adding hydrogen molecules to the ligand its showing dis kind of error before detecting torsion tree. so can't able to set number of torsion and still i cannot able to find SA.maps file in ma folder..please need help guyz...
Remove end-root in the pdbqt file of the ligand and see how it works.
there is no end-root in ligand.pdbqt file sir..only end branch is there
ENDBRANCH 3 4
ENDBRANCH 2 3
ENDBRANCH 1 2
I even deleted and tried but still it has not worked der is no SA.maps and cannot add hydrogen atoms to ligand...is it compulsary to add hydrogens to ligand...
Dear
As Rajanikant Bro said: To add above SA maps using MGL tools GUI follow file preparation protocol till saving Flex and Rigid file of Receptor. After this from Grid tab follow steps mentioned below
1. GRID >> MACRO-MOLECULE >> OPEN >> OPEN YOUR RIGID FILE.
2. SET MAP TYPES >> DIRECTLY >> by default you will find " A C HD N NA OA SA" in text widget and if not then write them manually and ACCEPT.
After that go to gpf file and add SA in both ligand_type and receptor_type and also add "map R_rigid.SA.map ". Now run autogrid, it goes fine.
1) If you create your pdb file with gaussview or any other incompatible program autodock can not recognize which atoms is which. I advise you to convert your pdb or mol2 file with Discovery Studio Visulaliser pdb again. Then in MGLTOOLs after opened your files you should do this:
Edit-->Atoms-->assign AD4 types
before saving your receptor and/or ligand as pdbqt file and before creating gpf and dpf file
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