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ccsb-scripps / AutoDock-GPU

AutoDock for GPUs and other accelerators
https://ccsb.scripps.edu/autodock
GNU General Public License v2.0
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autogrid4: FATAL ERROR: Sorry, I can't find or open AD4_parameters.dat #231

Closed amir-tagh closed 1 year ago

amir-tagh commented 1 year ago

Hello,

there is a Br atom in my ligand and I have copied the AD4_parameters.dat in the dir with autodock4 & autogrid4 exe and added the parameters to the .gpf file as following, but I am getting the error message:'

can you please let me know if I am doing it right to handle the heavy atoms.

Thanks, Amir

error

autogrid4: FATAL ERROR: Sorry, I can't find or open AD4_parameters.dat

.gpf file

parameter_file AD4_parameters.dat # AD4 for heavy atoms npts 100 100 100 # num.grid points in xyz gridfld protein.maps.fld # grid_data_file spacing 0.375 # spacing(A) receptor_types A C HD N OA SA # receptor atom types ligand_types B C HD N NA OA # ligand atom types receptor protein.pdbqt # macromolecule gridcenter auto # xyz-coordinates or auto smooth 0.5 # store minimum energy w/in rad(A) map protein.B.map # atom-specific affinity map map protein.C.map # atom-specific affinity map map protein.HD.map # atom-specific affinity map map protein.N.map # atom-specific affinity map map protein.NA.map # atom-specific affinity map map protein.OA.map # atom-specific affinity map elecmap protein.e.map # electrostatic potential map dsolvmap protein.d.map # desolvation potential map dielectric -0.1465 # <0, AD4 distance-dep.diel;>0, constant

diogomart commented 1 year ago

Hi, I think the path is relative to the current working directory, so you need to place the .dat file in the directory that autogrid is run from. Alternatively, it should be possible to specify the full path to the .dat file.

amir-tagh commented 1 year ago

Hi,

So, I changed the Br in the .dat file to B and autogrid worked. Now autodock_gpu_64wi is complaining about " atom with unknown type: A or B!". Is there a way around this?

Thanks,

error

CUDA Setup time 0.095693s Error: Ligand includes atom with unknown type: A or B!

diogomart commented 1 year ago

Which version (with commit ID) are you using? e.g.

$ ./autodock_gpu_128wi 
AutoDock-GPU version: v1.5.3-48-gf9ea8ba79f3cf73a7873357f949a0043c524ca2b
amir-tagh commented 1 year ago

it is: autodock_gpu_64wi --version AutoDock-GPU version: v1.4-release

diogomart commented 1 year ago

Updating should fix it.

amir-tagh commented 1 year ago

Can you please let me know how I can update the current version.

can not find any documents googling it.

https://catalog.ngc.nvidia.com/orgs/hpc/containers/autodock

amir-tagh commented 1 year ago

I made a new installation on HPC and it is working. Thanks!