ADL: Error in Autogrid

Van Dam, Hubertus hvandam at
Sat Apr 11 22:39:24 PDT 2020

Also make sure you are running a consistent set of tools. Autogrid and autogrid4 are not the same. For autogrid4 you need to be running tools prepare_receptor4, prepare_ligand4, etc. For autogrid you need to be running prepare_receptor, prepare_ligand, etc. 

A piece of advice regarding posting questions: Please provide as complete an error message as you can. I have no idea exactly which program you ran (autogrid or autogrid4? MGLTools is a collection of tools, which one produced error 1? What is error 1 or error 2? What tutorial instructions are you following?). I would expect that these tools produce some error text which would provide much more information about what the error is. Someone with experience running these tools might be able to explain what the error message actually means. The information you have provided offers very little to go on.

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

On 4/11/20, 23:35, "autodock-bounces at on behalf of Muzaffar Rehman" <autodock-bounces at on behalf of m.muzaffar687 at> wrote:

    There might be metals atoms in your protein structure. Remove those abd
    Dont forget to add polar hydrogens.
    On Sun, 12 Apr 2020 08:43 mukund ghavre, <muki_01 at> wrote:
    > Hi,I was unable to proceed with autogrid. I am following tutorial notes
    > for docking. When I tried to run autogrid, error 2 was shown in the cmd.At
    > the beginning when I opened MGL tools, error 1 was shown in cmd. I am not
    > sure what is wrong with my procedure?Can someone please help? I really need
    > to dock a molecule in one specific protein
    > urgently.Thanks,Mukund________________________________________________
    > --- ADL: AutoDock List  ---;!!P4SdNyxKAPE!RMNeCk9KmcwXZB4sHLoakr5HPmroYT_WQfELJPHkcK-QufkXrmBDNDS5ATsYxoA$  ---
    --- ADL: AutoDock List  ---;!!P4SdNyxKAPE!RMNeCk9KmcwXZB4sHLoakr5HPmroYT_WQfELJPHkcK-QufkXrmBDNDS5ATsYxoA$  ---

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