ADL: autogrid4: ERROR: Too many "map" keywords (15); the "ligand_types" command declares only 14 atom types

Diogo Martins diogo.stmart at gmail.com
Mon Apr 13 00:51:20 PDT 2020


Hi,

Looks like a bug with the "-d" option in "prepare_gpf4.py". It should work
fine if you use "-l" to process one ligand at a time.

Alternatively, you can write all atom types that occur in the ligands after
ligand_types in the .gpf file, followed by the "map" keywords in the same
order. This will calculate all the maps you'll need.

Best regards,

On Sun, 12 Apr 2020 at 04:17, venkat <azbvenkat at gmail.com> wrote:

> Dear Sir,
> I am trying to perform Autodock  for 120 ligands with single receptor  in
> Centos 7 (MGLTOOLS 1.5.7 <https://ccsb.scripps.edu/download/292/>),
> following commands I used in terminal to generate *gpf *file
>
> * pythonsh
>
> /home/subbu/MGLTools-1.5.6/MGLToolsPckgs/AutoDockTools/Utilities24/prepare_gpf4.py
> -d ../trterpene_pdb/
> -r plpro.pdbqt -p npts="40,40,40" -p gridcenter="-19.198,53.911,-34.169" -o
> grid.gpf*
> end: all_types =  C HD OAC HD OAC HD OAC HD OAC HD OAC HD OAC HD OAC HD OAC
> HD OAC HD OAC HD OAC OAC HD OAC HD OAC HD OAC HD OAC HD OAC HD OAA C HD OAC
> HD OAA C NA Zn OA N SA HDA C HD OAC HD OAC HD OAC HD OAA C HD OAC HD OAC HD
> OAC HD OAA C OAC HD OAC HD OAC HD OACC HD OAC HD OAC HD OAC HD OAC HD OAC
> NA OA N SA HDC OAC OAC HD OAHD SA C OA NA C HD OAC HD OAC HD OAC HD OAC HD
> OAC HD OAC HD OAC HD OAC HD OAA C OA N SA HDC HD OAC HD OAA C HD OACC HD
> OAA C Cl OA N SA HDC HD OAC HD OAC HD OAC HD OAHD SA C OA NC OAC HD OAC HD
> OAC HD OAC HD OACC HD OAC HD OAA C OAC HD OAC HD OAC HD OAC HD OAC HD OAC
> HD OAC HD OAC HD OAA C HD OAC HD OAA C HD OAC HD OAC HD OAC HD OAC HD OAC
> HD OAC HD OAC HD OAC HD OAC HD OAC HD OAC HD OAC HD OAC HD OAC HD OAA C HD
> OAHD C OA BrC OAA C HD OAC HD OAA C HD OAC HD OAC HD OAC HD OAA C HD OAC HD
> OAC HD OAA C HD OAC HD OACC HD OACC HD OAC OAA C HD OAA C HD OAC HD OAC HD
> OAC HD OA
>
> I tried to run autogrid4
>
>  *autogrid4 -p grid.gpf -l grid.glg*
> autogrid4: WARNING:  Unrecognized keyword in grid parameter file.
> autogrid4: WARNING:  Unrecognized keyword in grid parameter file.
> *autogrid4: ERROR:  Too many "map" keywords (15);  the "ligand_types"
> command declares only 14 atom types.*
> Remove a "map" keyword from the GPF.
>
> *some how i **understood** many repeating  same type **atom-type**, to *
> *handle** situation and **preceded** further kindly requesting your *
> *guidance. *
> Herewith I attached the grid.gpf file for your reference.
>
> Thank you very much
>
> Yours Sincerely,
> *S.VENKATESH  *
> ________________________________________________
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