[Chimera-users] using the Chimera "AutoDock Vina" tool

[Elaine Meng]

Hi Tanara,
Not a bug…. the error message is telling you the problem, that in the Autodock Vina dialog, you have the receptor and ligand set to the same model. The dialog has something like this in it:

Receptor: [what you chose as receptor]
Ligand: [what you chose as ligand]

Make sure that the receptor is set to what you want, probably 3dbs.pdb (#0), and that the ligand is set to what you want, probably #1, before you click “OK” or “Apply”.

You can see the help for the tool by clicking the “Help” button, or view the copy on our website here:
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/vina/vina.html>

This e-mail address  chimera-users at cgl.ucsf.edu  is the one to use for questions.
I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Aug 8, 2019, at 7:50 PM, Tanara Arenhart <tanara.arenhart at catolicasc.org.br> wrote:
> 
> The following bug report has been submitted:
> Platform:        Windows64 (WGL) Microsoft Windows Unknown 10.0 (Build 17134) x64
> Chimera Version: 1.13.1_b41965
> Description
> Hi!
> 
> I'm trying to dock my protein with a ligand, but everytime appears this message: "receptor and ligand cannot be the same model".
> 
> I don't know why, because i'm doing the same things I always do. What could be happening?
> 
> Thank you!
> 
> Open models
> #0 3dbs.pdb
> #1 smiles:CC1CCC2C3(CCC(...
> #2 AutoDock Vina Search Volume
> 
> 
> Reply log:
> Failed to translate SMILES to 3D structure via NCI web service (SMILES: receptor and ligand cannot be the same model)
> Failed to translate SMILES to 3D structure via Indiana University web service (SMILES: receptor and ligand cannot be the same model)
> Web services failed to translate SMILES string to 3D structure.
> 
> Translated SMILES to 3D structure via NCI web service (SMILES: CC1CCC2C3(CCC(C(C3CCC2(C14CC5=C(O4)C(=CC(=O)C5=O)C)C)(C)C)O)C)
> No incomplete side chains
> Chain-initial residues that are actual N terminii: 
> Chain-initial residues that are not actual N terminii: 
> Chain-final residues that are actual C terminii: 
> Chain-final residues that are not actual C terminii: 
> 0 hydrogen bonds
> Hydrogens added
> Charge model: AMBER ff14SB
> Assigning partial charges to residue STP (net charge +0) with gasteiger method
> Running ANTECHAMBER command: C:/Program Files/Chimera 1.13.1/bin/amber16/bin\antechamber -i c:\users\nara_\appdata\local\temp\tmpi9opye\ante.in.mol2 -fi mol2 -o c:\users\nara_\appdata\local\temp\tmpi9opye\ante.out.mol2 -fo mol2 -c gas -nc 0 -j 5 -s 2 -dr n
> (STP) 
> 
> (STP) Welcome to antechamber 17.3: molecular input file processor.
> 
> (STP) 
> 
> (STP) Info: Finished reading file (c:\users\nara_\appdata\local\temp\tmpi9opye\ante.in.mol2).
> 
> (STP) Running: "C:/Program Files/Chimera 1.13.1/bin/amber16/bin/bondtype" -j part -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac
> 
> (STP) 
> 
> (STP) 
> 
> (STP) Running: "C:/Program Files/Chimera 1.13.1/bin/amber16/bin/atomtype" -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff
> 
> (STP) Running: "C:/Program Files/Chimera 1.13.1/bin/amber16/bin/atomtype" -i ANTECHAMBER_GAS.AC -o ANTECHAMBER_GAS_AT.AC -d "C:/Program Files/Chimera 1.13.1/bin/amber16/dat/antechamber/ATOMTYPE_GAS.DEF"
> 
> (STP) 
> 
> Charges for residue STP determined
> Total charge for #0: 0.000
> #0, chain A: phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit γ isoform
> Traceback (most recent call last):
> File "C:\Program Files\Chimera 1.13.1\share\chimera\preferences\base.py", line 447, in save
> WindowsError: [Error 32] O arquivo j� est� sendo usado por outro processo
> Cannot replace previous preferences file: C:\Users\nara_\AppData\Roaming\.chimera\preferences:
> WindowsError: [Error 32] O arquivo j� est� sendo usado por outro processo
> 
> File "C:\Program Files\Chimera 1.13.1\share\chimera\preferences\base.py", line 447, in save
> 
> See reply log for Python traceback.
> 
> 
> Residues with incomplete side chains:
> 	MET 143.A
> 	GLU 322.A
> Replacing each by 'swapaa same (residue atom spec) lib Dunbrack preserve True'
> MET 143.A: phi none, psi -122.2 trans
> Chi angles for MET 143.A:
> GLU 322.A: phi -130.9, psi 172.4 trans
> Chi angles for GLU 322.A:
> Applying GLU rotamer (chi angles: -62.4 -179.4 -3.8) to GLU 322.A
> Applying MET rotamer (chi angles: -65.8 -61.8 -69.4) to MET 143.A
> Terminii for 3dbs.pdb (#0) chain A determined from SEQRES records
> Chain-initial residues that are actual N terminii: MET 143.A
> Chain-initial residues that are not actual N terminii: GLU 267.A, CYS 357.A, LEU 460.A, PHE 497.A, HIS 525.A, ARG 544.A, GLU 981.A
> Chain-final residues that are actual C terminii: 
> Chain-final residues that are not actual C terminii: ALA 253.A, GLU 322.A, CYS 435.A, GLY 489.A, ASN 522.A, ALA 528.A, HIS 967.A, VAL 1091.A
> 718 hydrogen bonds
> Adding 'H' to GLU 267.A
> Adding 'H' to CYS 357.A
> Adding 'H' to LEU 460.A
> Adding 'H' to PHE 497.A
> Adding 'H' to HIS 525.A
> Adding 'H' to ARG 544.A
> Adding 'H' to GLU 981.A
> Removing spurious proton from 'C' of VAL 1091.A
> Hydrogens added
> Charge model: AMBER ff14SB
> Total charge for #0: -8.000
> receptor and ligand cannot be the same model
> receptor and ligand cannot be the same model
> 
> 
> 
> 
> OpenGL Vendor: Intel
> OpenGL Renderer: Intel(R) HD Graphics
> OpenGL Version: 4.4.0 - Build 20.19.15.4835
> Manufacturer: Dell Inc.
> Model: Inspiron 5452
> TotalPhysicalMemory: 4203823104
> 
> ――――――――――――――――――――
> Multisampling: False
> Shadows: False
> Shadow texture size: 2048
> Silhouettes: False
> Depth cue: True
> Subdivision quality: 1.50
> Single-layer transparency: True
> Transparent background: False
> Shaders supported: True
> Using shader: True
> Window size: 1366 663
> Camera mode: mono
> Orthographic projection: False
> Center of rotation: front center
> Near/far clipping: False
> Key light: True
> Fill light: True
> Back light: False
> Ambient light: 0.20
> Specular sharpness: 30.00
> Specular reflectivity: 1.00
> 
> ――――――――――――――――――――
> AntialiasLines: native
> AntialiasPoints: native
> BlendEquation: native
> BlendFuncSeparate: native
> BrokenAttribLocation: native, disabled
> ChoosePixelFormat: extension
> ColorTable: not supported
> CompileAndExecute: native
> CompiledVertexArray: extension
> CubeMap: native
> CullVertex: not supported
> DrawElementsInstanced: native, disabled
> DrawRangeElements: native
> FBConfig: not supported
> FBOShadows: native
> FastMultisampling: native, disabled
> FramebufferMultisample: native
> FramebufferObject: native
> LimitVertexAttribDivisor: native, disabled
> Multisample: native
> Multitexture: native
> PackedDepthStencil: native
> PalettedTexture: not supported
> PointParameters: native
> SeamlessCubeMap: native
> SeparateSpecularColor: native
> Shading: native
> Shadows: native
> StereoMultisample: native
> StereoRubberBanding: native
> Texture3D: native
> TextureColorTable: not supported
> TextureEdgeClamp: native
> TrustColorLogicBlend: native
> TrustNormals: native
> VertexArray: native
> VertexAttrib: native
> VertexAttribDivisor: native
> VertexBufferObject: native, disabled
> WindowPos: not supported
> 
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