[Chimera-users] Chimera bug report submission

[Tanara Arenhart]

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