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error - atom types in PDBQT and GPF
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Author:  bwinborn [ Wed Oct 07, 2015 6:33 pm ]
Post subject:  error - atom types in PDBQT and GPF

Hi all,

I am getting an error when running Autogrid on AutoDock Tools:

ERROR: The number of atom types found in the receptor PDBQT (7) does not match the number specified by the "receptor_types" command (6) in the GPF!

However, there are actually only 6 atom types in the pdbqt. I also noticed in the .glg file that the atom types are numbered 0, 1, 3, 4, 5, and 6. There is no atom type 2. I guess 2 is getting skipped for some reason. Could this be causing the error? I have attached the .pdbqt and .glg.

Any suggestions would be greatly appreciated. Thanks!

Brett

Attachments:
4OEA.glg [225.72 KiB]
Downloaded 380 times
4OEA.pdbqt [189.45 KiB]
Downloaded 383 times

Author:  Ruth Huey [ Mon Dec 07, 2015 7:25 pm ]
Post subject:  Re: error - atom types in PDBQT and GPF

It appears that the grid parameter file you used for your autogrid4 calculation was incomplete:
It only contains these 6 parameters: npts, gridfld, spacing, receptor_types, ligand_types

Missing parameters include:
receptor, gridcenter, smooth along with all the output map filenames:
GPF> map 4OEA.A.map # atom-specific affinity map
GPF> map 4OEA.C.map # atom-specific affinity map
GPF> map 4OEA.Cl.map # atom-specific affinity map
GPF> map 4OEA.OA.map # atom-specific affinity map
GPF> map 4OEA.N.map # atom-specific affinity map
GPF> map 4OEA.HD.map # atom-specific affinity map
GPF> elecmap 4OEA.e.map # electrostatic potential map
GPF> dsolvmap 4OEA.d.map # desolvation potential map
GPF> dielectric -0.1465 # <0, AD4 distance-dep.diel;>0, constant

Author:  bwinborn [ Mon Dec 14, 2015 7:18 pm ]
Post subject:  Re: error - atom types in PDBQT and GPF

Ruth Huey,

Thank you so much for the reply. I will see if I can figure it out with the new info. Thanks!

Brett

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