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

Van Dam, Hubertus hvandam at bnl.gov
Mon Apr 13 06:59:45 PDT 2020


Hi,

You have very many ligand types, many of which are repeated many times. I think you'll do much better if you just list the unique ligand types. If you really have to have many ligand types then there is a compile time parameter that you can increase (this does increase the memory requirements for the autogrid4 and autodock4 programs). This variable is MAX_ATOM_TYPES in autocomm.h. You will have to recompile both autogrid4 and autodock4.

Best wishes,

    Huub

-----------------------------------------------------------------------------------------------------
Hubertus van Dam, 631-344-6020, hvandam at bnl.gov
Brookhaven National Laboratory
 

On 4/12/20, 07:19, "autodock-bounces at scripps.edu on behalf of venkat" <autodock-bounces at scripps.edu on behalf of 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://urldefense.com/v3/__https://ccsb.scripps.edu/download/292/__;!!P4SdNyxKAPE!RQsrU3rPtFQ-NNHUvJRPiwbQ5jzh8QD1AbkMf2VoXBYmqJa3F3jQqksEPKOBXqg$ >),
    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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