ADL: Autogrid4 error

Garrett M. Morris garrett at scripps.edu
Tue Jan 15 16:54:55 PST 2008


This line in your GPF is causing the problem:

> GPF> receptor_types C H N O S             # receptor atom types


There are no "O" atom types in AutoDock 4, only "OA" and "OS".  See  
the parameter file in this FAQ:

	http://autodock.scripps.edu/faqs-help/faq/where-do-i-set-the-autodock-4-force-field-parameters

Make sure you prepared your receptor properly in ADT, saving it as a  
PDBQT file for AutoGrid and AutoDock 4.

On 15 Jan, 2008, at 7:54 am, Monica Chhabra wrote:

> Hi Autodockers:
>
> I am trying to do rigid-flex docking with Autodock4.  I
> am doing all the steps as in the  
> tutorial(UsingAutoDock4WithADT_1.4.5b.pdf I downloaded from website)  
> I prepared the pdbqt file for macromolecule using
> File-> Save-> Write PDBQT.
> I have ignored - Preparing the flexible residue file exercise from  
> the tutorial(since I am not doing flex-flex docking).  I also  
> prepared ligand pdbqt file.
> I get the the following error when I try to run autorid4:
> ERROR:  Unknown receptor type: "O"
> -- Add parameters for it to the parameter library first!
>
> I am attaching that error file for details.  Has anyone encountered  
> similar problem?
> I really appreciate any help with this.
>
> Thanks,
> Monica
> _______________________________________________________
>
> __________//____________________________/////_________________/ 
> ________
> _________/__/____________/_____________/______________/_______/ 
> ________
> ________/____/___________/_____________/______________________/ 
> ________
> ________/____/__/_____/_/////___/////__/__////_/_///__/__////_/ 
> ________
> _______/______/_/_____/__/_____/_____/_/_____/_//___/_/_/____// 
> ________
> _______////////_/_____/__/_____/_____/_/_____/_/______/_/_____/ 
> ________
> _______/______/_/____//__/___/_/_____/_/_____/_/______/_/____// 
> ________
> _______/______/__////_/___///___/////___/////__/______/__////_/ 
> ________
>
>       _______________________________________________________
>
>                                ______
>                               /      \
>                              /        \
>                             /          \
>                             \    /\    /
>                              \  /  \  /
>                               \/ /\ \/
>                                 /  \
>                                /____\
>
>
>                ______________________________________
>               |                                      |
>               |            AutoGrid 4.00             |
>               |                                      |
>               |        Garrett M. Morris, TSRI       |
>               |            Ruth Huey, TSRI           |
>               |        David S. Goodsell, TSRI       |
>               |         Arthur J. Olson, TSRI        |
>               |                                      |
>               |        (c) 1989-2005, TSRI           |
>               |   The Scripps Research Institute     |
>               |______________________________________|
>
>                ______________________________________
>               |                                      |
>               | Calculation of van der Waals, H-Bond,|
>               |   Electrostatic Potential Energy, &  |
>               |   Desolvation Free Energy Grid Maps  |
>               |             for AutoDock             |
>               |______________________________________|
>
>
>
>
>                           $Revision: 1.58 $
>
>
>
> Maximum number of maps that can be computed = 22 (defined by  
> MAX_MAPS in "autocomm.h").
>
>
> This file was created at:                       0:39 52" a.m.,  
> 01/14/2008
>                   using:                       "bmi-xeon1-01"
>
>
> Setting up parameter library with factory defaults.
>
>
> Free energy coefficient for the van der Waals term =    0.1560
>
> Free energy coefficient for the H-bonding term     =    0.0974
>
> Free energy coefficient for the electrostatic term =    0.1465
>
> Free energy coefficient for the desolvation term   =    0.1159
>
> Free energy coefficient for the torsional term     =    0.2744
>
> Parameters for the atom type named "H" were read in from the  
> parameter library as follows:
>        R-eqm = 2.00 Angstrom,  weighted epsilon = 0.003,   
> At.frag.vol. = 0.000,  At.solv.par. = 0.001,
>        Hb R-eqm = 0.000,  weighted Hb epsilon = 0.000,  Hb type =  
> 0,  bond index = 3
>
> Parameters for the atom type named "HD" were read in from the  
> parameter library as follows:
>        R-eqm = 2.00 Angstrom,  weighted epsilon = 0.003,   
> At.frag.vol. = 0.000,  At.solv.par. = 0.001,
>        Hb R-eqm = 0.000,  weighted Hb epsilon = 0.000,  Hb type =  
> 2,  bond index = 3
>
> Parameters for the atom type named "HS" were read in from the  
> parameter library as follows:
>        R-eqm = 2.00 Angstrom,  weighted epsilon = 0.003,   
> At.frag.vol. = 0.000,  At.solv.par. = 0.001,
>        Hb R-eqm = 0.000,  weighted Hb epsilon = 0.000,  Hb type =  
> 1,  bond index = 3
>
> Parameters for the atom type named "C" were read in from the  
> parameter library as follows:
>        R-eqm = 4.00 Angstrom,  weighted epsilon = 0.023,   
> At.frag.vol. = 33.510,  At.solv.par. = -0.001,
>        Hb R-eqm = 0.000,  weighted Hb epsilon = 0.000,  Hb type =  
> 0,  bond index = 0
>
> Parameters for the atom type named "A" were read in from the  
> parameter library as follows:
>        R-eqm = 4.00 Angstrom,  weighted epsilon = 0.023,   
> At.frag.vol. = 33.510,  At.solv.par. = -0.001,
>        Hb R-eqm = 0.000,  weighted Hb epsilon = 0.000,  Hb type =  
> 0,  bond index = 0
>
> Parameters for the atom type named "N" were read in from the  
> parameter library as follows:
>        R-eqm = 3.50 Angstrom,  weighted epsilon = 0.025,   
> At.frag.vol. = 22.449,  At.solv.par. = -0.002,
>        Hb R-eqm = 0.000,  weighted Hb epsilon = 0.000,  Hb type =  
> 0,  bond index = 1
>
> Parameters for the atom type named "NA" were read in from the  
> parameter library as follows:
>        R-eqm = 3.50 Angstrom,  weighted epsilon = 0.025,   
> At.frag.vol. = 22.449,  At.solv.par. = -0.002,
>        Hb R-eqm = 1.900,  weighted Hb epsilon = 0.487,  Hb type =  
> 4,  bond index = 1
>
> Parameters for the atom type named "NS" were read in from the  
> parameter library as follows:
>        R-eqm = 3.50 Angstrom,  weighted epsilon = 0.025,   
> At.frag.vol. = 22.449,  At.solv.par. = -0.002,
>        Hb R-eqm = 1.900,  weighted Hb epsilon = 0.487,  Hb type =  
> 3,  bond index = 1
>
> Parameters for the atom type named "OA" were read in from the  
> parameter library as follows:
>        R-eqm = 3.20 Angstrom,  weighted epsilon = 0.031,   
> At.frag.vol. = 17.157,  At.solv.par. = -0.003,
>        Hb R-eqm = 1.900,  weighted Hb epsilon = 0.487,  Hb type =  
> 5,  bond index = 2
>
> Parameters for the atom type named "OS" were read in from the  
> parameter library as follows:
>        R-eqm = 3.20 Angstrom,  weighted epsilon = 0.031,   
> At.frag.vol. = 17.157,  At.solv.par. = -0.003,
>        Hb R-eqm = 1.900,  weighted Hb epsilon = 0.487,  Hb type =  
> 3,  bond index = 2
>
> Parameters for the atom type named "F" were read in from the  
> parameter library as follows:
>        R-eqm = 3.09 Angstrom,  weighted epsilon = 0.012,   
> At.frag.vol. = 15.448,  At.solv.par. = -0.001,
>        Hb R-eqm = 0.000,  weighted Hb epsilon = 0.000,  Hb type =  
> 0,  bond index = 4
>
> Parameters for the atom type named "Mg" were read in from the  
> parameter library as follows:
>        R-eqm = 1.30 Angstrom,  weighted epsilon = 0.137,   
> At.frag.vol. = 1.560,  At.solv.par. = -0.001,
>        Hb R-eqm = 0.000,  weighted Hb epsilon = 0.000,  Hb type =  
> 0,  bond index = 4
>
> Parameters for the atom type named "MG" were read in from the  
> parameter library as follows:
>        R-eqm = 1.30 Angstrom,  weighted epsilon = 0.137,   
> At.frag.vol. = 1.560,  At.solv.par. = -0.001,
>        Hb R-eqm = 0.000,  weighted Hb epsilon = 0.000,  Hb type =  
> 0,  bond index = 4
>
> Parameters for the atom type named "P" were read in from the  
> parameter library as follows:
>        R-eqm = 4.20 Angstrom,  weighted epsilon = 0.031,   
> At.frag.vol. = 38.792,  At.solv.par. = -0.001,
>        Hb R-eqm = 0.000,  weighted Hb epsilon = 0.000,  Hb type =  
> 0,  bond index = 5
>
> Parameters for the atom type named "SA" were read in from the  
> parameter library as follows:
>        R-eqm = 4.00 Angstrom,  weighted epsilon = 0.031,   
> At.frag.vol. = 33.510,  At.solv.par. = -0.002,
>        Hb R-eqm = 2.500,  weighted Hb epsilon = 0.097,  Hb type =  
> 5,  bond index = 6
>
> Parameters for the atom type named "S" were read in from the  
> parameter library as follows:
>        R-eqm = 4.00 Angstrom,  weighted epsilon = 0.031,   
> At.frag.vol. = 33.510,  At.solv.par. = -0.002,
>        Hb R-eqm = 0.000,  weighted Hb epsilon = 0.000,  Hb type =  
> 0,  bond index = 6
>
> Parameters for the atom type named "Cl" were read in from the  
> parameter library as follows:
>        R-eqm = 4.09 Angstrom,  weighted epsilon = 0.043,   
> At.frag.vol. = 35.824,  At.solv.par. = -0.001,
>        Hb R-eqm = 0.000,  weighted Hb epsilon = 0.000,  Hb type =  
> 0,  bond index = 4
>
> Parameters for the atom type named "CL" were read in from the  
> parameter library as follows:
>        R-eqm = 4.09 Angstrom,  weighted epsilon = 0.043,   
> At.frag.vol. = 35.824,  At.solv.par. = -0.001,
>        Hb R-eqm = 0.000,  weighted Hb epsilon = 0.000,  Hb type =  
> 0,  bond index = 4
>
> Parameters for the atom type named "Ca" were read in from the  
> parameter library as follows:
>        R-eqm = 1.98 Angstrom,  weighted epsilon = 0.086,   
> At.frag.vol. = 2.770,  At.solv.par. = -0.001,
>        Hb R-eqm = 0.000,  weighted Hb epsilon = 0.000,  Hb type =  
> 0,  bond index = 4
>
> Parameters for the atom type named "CA" were read in from the  
> parameter library as follows:
>        R-eqm = 1.98 Angstrom,  weighted epsilon = 0.086,   
> At.frag.vol. = 2.770,  At.solv.par. = -0.001,
>        Hb R-eqm = 0.000,  weighted Hb epsilon = 0.000,  Hb type =  
> 0,  bond index = 4
>
> Parameters for the atom type named "Mn" were read in from the  
> parameter library as follows:
>        R-eqm = 1.30 Angstrom,  weighted epsilon = 0.137,   
> At.frag.vol. = 2.140,  At.solv.par. = -0.001,
>        Hb R-eqm = 0.000,  weighted Hb epsilon = 0.000,  Hb type =  
> 0,  bond index = 4
>
> Parameters for the atom type named "MN" were read in from the  
> parameter library as follows:
>        R-eqm = 1.30 Angstrom,  weighted epsilon = 0.137,   
> At.frag.vol. = 2.140,  At.solv.par. = -0.001,
>        Hb R-eqm = 0.000,  weighted Hb epsilon = 0.000,  Hb type =  
> 0,  bond index = 4
>
> Parameters for the atom type named "Fe" were read in from the  
> parameter library as follows:
>        R-eqm = 1.30 Angstrom,  weighted epsilon = 0.002,   
> At.frag.vol. = 1.840,  At.solv.par. = -0.001,
>        Hb R-eqm = 0.000,  weighted Hb epsilon = 0.000,  Hb type =  
> 0,  bond index = 4
>
> Parameters for the atom type named "FE" were read in from the  
> parameter library as follows:
>        R-eqm = 1.30 Angstrom,  weighted epsilon = 0.002,   
> At.frag.vol. = 1.840,  At.solv.par. = -0.001,
>        Hb R-eqm = 0.000,  weighted Hb epsilon = 0.000,  Hb type =  
> 0,  bond index = 4
>
> Parameters for the atom type named "Zn" were read in from the  
> parameter library as follows:
>        R-eqm = 1.48 Angstrom,  weighted epsilon = 0.086,   
> At.frag.vol. = 1.700,  At.solv.par. = -0.001,
>        Hb R-eqm = 0.000,  weighted Hb epsilon = 0.000,  Hb type =  
> 0,  bond index = 4
>
> Parameters for the atom type named "ZN" were read in from the  
> parameter library as follows:
>        R-eqm = 1.48 Angstrom,  weighted epsilon = 0.086,   
> At.frag.vol. = 1.700,  At.solv.par. = -0.001,
>        Hb R-eqm = 0.000,  weighted Hb epsilon = 0.000,  Hb type =  
> 0,  bond index = 4
>
> Parameters for the atom type named "Br" were read in from the  
> parameter library as follows:
>        R-eqm = 4.33 Angstrom,  weighted epsilon = 0.061,   
> At.frag.vol. = 42.566,  At.solv.par. = -0.001,
>        Hb R-eqm = 0.000,  weighted Hb epsilon = 0.000,  Hb type =  
> 0,  bond index = 4
>
> Parameters for the atom type named "BR" were read in from the  
> parameter library as follows:
>        R-eqm = 4.33 Angstrom,  weighted epsilon = 0.061,   
> At.frag.vol. = 42.566,  At.solv.par. = -0.001,
>        Hb R-eqm = 0.000,  weighted Hb epsilon = 0.000,  Hb type =  
> 0,  bond index = 4
>
> Parameters for the atom type named "I" were read in from the  
> parameter library as follows:
>        R-eqm = 4.72 Angstrom,  weighted epsilon = 0.086,   
> At.frag.vol. = 55.059,  At.solv.par. = -0.001,
>        Hb R-eqm = 0.000,  weighted Hb epsilon = 0.000,  Hb type =  
> 0,  bond index = 4
>
> GPF> npts 78 50 45                        # num.grid points in xyz
> /usr/local/autodock-4.0.1/bin/autogrid4: Number of grid elements  
> must be even; z-elements changed to: 44
>
> Number of grid points in x-direction:   79
> Number of grid points in y-direction:   51
> Number of grid points in z-direction:   45
>
> GPF> gridfld VA387_P_dimer_only_2OBS.maps.fld # grid_data_file
>
> Creating (AVS-readable) grid maps file :  
> VA387_P_dimer_only_2OBS.maps.fld
>
> Creating (AVS-readable) grid-coordinates extrema file :  
> VA387_P_dimer_only_2OBS.maps.xyz
>
> GPF> spacing 0.375                        # spacing(A)
> Grid Spacing :                  0.375 Angstrom
>
> GPF> receptor_types C H N O S             # receptor atom types
>
> /usr/local/autodock-4.0.1/bin/autogrid4: ERROR:  Unknown receptor  
> type: "O"
> -- Add parameters for it to the parameter library first!
>
>
>
> /usr/local/autodock-4.0.1/bin/autogrid4: ERROR:  Unknown receptor  
> type: "O"
> -- Add parameters for it to the parameter library first!
>
>
>
> /usr/local/autodock-4.0.1/bin/autogrid4: ERROR:  Unsuccessful  
> completion.
>
>
>
>
> /usr/local/autodock-4.0.1/bin/autogrid4: ERROR:  Unsuccessful  
> completion.
>
> ________________________________________________
> --- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list  
> ---

___
Dr Garrett M. Morris, M.A. (Oxon.), D.Phil. (Oxon.)

The Scripps Research Institute,       tel: (858) 784-2292
Dept. Molecular Biology,  MB-5,       fax: (858) 784-2860
10550  North Torrey Pines Road,       email: garrett at scripps.edu
La Jolla,  CA 92037-1000,  USA.       mgl.scripps.edu/people/gmm






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