Despite troubleshooting, repeatedly getting common error

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[PyRx is no longer developed at MGL]

Despite troubleshooting, repeatedly getting common error

Postby sreiling » Thu Aug 15, 2013 6:50 pm

I will spare you my feeble efforts, and just post the dlg file:

AutoDock 4.2 Release 4.2.5.1
(C) 1989-2012 The Scripps Research Institute
AutoDock comes with ABSOLUTELY NO WARRANTY.
AutoDock is free software, and you are welcome
to redistribute it under certain conditions;
for details type 'autodock4 -C'

main.cc $Revision: 1.194 $

Compiled on Dec 14 2012 at 12:07:30


This file was created at: 1:40 41" p.m., 08/15/2013
using: "XXXXXXX-PC"

________________________________________________________________

SETTING UP DEFAULT PARAMETER LIBRARY
________________________________________________________________


Random number generator was seeded with values 5364, 1376592041.
Docking parameter file (DPF) used for this docking: 2XDA_A_apo_rigid_7124.dpf
DPF> autodock_parameter_version 4.2 # used by autodock to validate parameter set

Autodock parameter version 4.2.
DPF> outlev 1 # diagnostic output level

Output Level = 1 ADT-COMPATIBLE OUTPUT DURING DOCKING.
DPF> intelec # calculate internal electrostatics

Electrostatic energies will be calculated for all non-bonds between moving atoms.
DPF> seed pid time # seeds for random generator

Random number generator was seeded with values 5364, 1376592041.
DPF> ligand_types A C OA HD N # atoms types in ligand

DPF> fld ..\2XDA_A_apo_rigid.maps.fld # grid_data_file

Opening Grid Map Dimensions file: ..\2XDA_A_apo_rigid.maps.fld
Grid Point Spacing = 0.375 Angstroms

Even Number of User-specified Grid Points = 50 x-points
74 y-points
70 z-points

Coordinates of Central Grid Point of Maps = (0.485, 19.144, 28.264)
Macromolecule file used to create Grid Maps = 2XDA_A_apo_rigid.pdbqt
Grid Parameter file used to create Grid Maps = 2XDA_A_apo_rigid.gpf
Minimum coordinates in grid = (-8.890, 5.269, 15.139)
Maximum coordinates in grid = (9.860, 33.019, 41.389)

DPF> map ..\2XDA_A_apo_rigid.A.map # atom-specific affinity map

D:\Program Files (x86)\The Scripps Research Institute\AutoDock\4.2.5.1\autodock4.exe: WARNING: Filename mismatch: "2XDA_A_apo_rigid.maps.fld" :: "..\2XDA_A_apo_rigid.maps.fld"
DPF> map ..\2XDA_A_apo_rigid.C.map # atom-specific affinity map

D:\Program Files (x86)\The Scripps Research Institute\AutoDock\4.2.5.1\autodock4.exe: WARNING: Filename mismatch: "2XDA_A_apo_rigid.maps.fld" :: "..\2XDA_A_apo_rigid.maps.fld"
DPF> map ..\2XDA_A_apo_rigid.OA.map # atom-specific affinity map

D:\Program Files (x86)\The Scripps Research Institute\AutoDock\4.2.5.1\autodock4.exe: WARNING: Filename mismatch: "2XDA_A_apo_rigid.maps.fld" :: "..\2XDA_A_apo_rigid.maps.fld"
DPF> map ..\2XDA_A_apo_rigid.HD.map # atom-specific affinity map

D:\Program Files (x86)\The Scripps Research Institute\AutoDock\4.2.5.1\autodock4.exe: WARNING: Filename mismatch: "2XDA_A_apo_rigid.maps.fld" :: "..\2XDA_A_apo_rigid.maps.fld"
DPF> map ..\2XDA_A_apo_rigid.N.map # atom-specific affinity map

D:\Program Files (x86)\The Scripps Research Institute\AutoDock\4.2.5.1\autodock4.exe: WARNING: Filename mismatch: "2XDA_A_apo_rigid.maps.fld" :: "..\2XDA_A_apo_rigid.maps.fld"
DPF> elecmap ..\2XDA_A_apo_rigid.e.map # electrostatics map

D:\Program Files (x86)\The Scripps Research Institute\AutoDock\4.2.5.1\autodock4.exe: WARNING: Filename mismatch: "2XDA_A_apo_rigid.maps.fld" :: "..\2XDA_A_apo_rigid.maps.fld"
DPF> desolvmap ..\2XDA_A_apo_rigid.d.map # desolvation map

D:\Program Files (x86)\The Scripps Research Institute\AutoDock\4.2.5.1\autodock4.exe: WARNING: Filename mismatch: "2XDA_A_apo_rigid.maps.fld" :: "..\2XDA_A_apo_rigid.maps.fld"
DPF> move ..\..\..\Ligands\7124.pdbqt # small molecule

1,4-interactions will be _ignored_ in the non-bonded internal energy calculation.

Ligand PDBQT file = "..\..\..\Ligands\7124.pdbqt"

Real= 1.26, CPU= 1.22, System= 0.03
D:\Program Files (x86)\The Scripps Research Institute\AutoDock\4.2.5.1\autodock4.exe: I'm sorry; I can't find or open "..\2XDA_A_apo_flex.pdbqt"
D:\Program Files (x86)\The Scripps Research Institute\AutoDock\4.2.5.1\autodock4.exe: FATAL ERROR: D:\Program Files (x86)\The Scripps Research Institute\AutoDock\4.2.5.1\autodock4.exe: I'm sorry; I can't find or open "..\2XDA_A_apo_flex.pdbqt"

D:\Program Files (x86)\The Scripps Research Institute\AutoDock\4.2.5.1\autodock4.exe: Unsuccessful Completion.
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sreiling
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Re: Despite troubleshooting, repeatedly getting common error

Postby sargis » Sat Aug 17, 2013 2:16 pm

sreiling wrote:I will spare you my feeble efforts, and just post the dlg file:

Sorry about that. Please try 0.9 version of PyRx; there has been quite a few bug fixes since 0.8 release. Version 0.8 isn't able to handle certain type of receptors with HETATM records. I don't know if you are getting this error because of that, but I can support you if there are any issues with the latest version of PyRx.
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