I am following this tutorial: http://cgmartini.nl/index.php/martini-3-tutorials/small-molecule-binding
and I came across this error:
So while adding dihedral corrections to Martini topology using ./bbsc.sh Protein_A.itp 181L.pdb, the resulting .itp file show the following error being appended to the .itp file:
ERROR) BaseMolecule: Cannot bond atom 0 to itself.
ERROR) BaseMolecule: Cannot bond atom 0 to itself.
ERROR) BaseMolecule: Cannot bond atom 0 to itself.
ERROR) BaseMolecule: Cannot bond atom 0 to itself.
ERROR) BaseMolecule: Cannot bond atom 0 to itself.
ERROR) BaseMolecule: Cannot bond atom 0 to itself.
ERROR) BaseMolecule: Cannot bond atom 0 to itself.
ERROR) BaseMolecule: Cannot bond atom 0 to itself.
ERROR) BaseMolecule: Cannot bond atom 0 to itself.
ERROR) BaseMolecule: Cannot bond atom 0 to itself.
ERROR) BaseMolecule: Cannot bond atom 0 to itself.
moving CA and CB to center of mass of BB, SC1 bead
measuring SC BB BB SC dihedrals
[ dihedrals ]
; SC-BB-BB-SC dihedrals
can't read "rsd": no such variable
On running vmd in my system I get the follwing warnings:
/usr/local/lib/vmd/vmd_LINUXAMD64: /usr/lib/x86_64-linux-gnu/libGL.so.1: no version information available (required by /usr/local/lib/vmd/vmd_LINUXAMD64)
followed by
Info) Multithreading available, 8 CPUs detected.
Info) CPU features: SSE2 AVX AVX2 FMA
Info) Free system memory: 1175MB (14%)
Info) No CUDA accelerator devices available.
Warning) Detected X11 'Composite' extension: if incorrect display occurs
Warning) try disabling this X server option. Most OpenGL drivers
Warning) disable stereoscopic display when 'Composite' is enabled.
Info) OpenGL renderer: Mesa DRI Intel(R) UHD Graphics 620 (Kabylake GT2)
Info) Features: STENCIL MSAA(4) MDE CVA MTX NPOT PP PS GLSL(OVFS)
Info) Full GLSL rendering mode is available.
Info) Textures: 2-D (16384x16384), 3-D (512x512x512), Multitexture (8)
Info) Dynamically loaded 2 plugins in directory:
Info) /usr/local/lib/vmd/plugins/LINUXAMD64/molfile
This is not an issue of vermouth/martinize, but has to do with the script bbsc.sh (which I don't know). Please refer to the martini forum for questions related to the tutorials.
I am following this tutorial: http://cgmartini.nl/index.php/martini-3-tutorials/small-molecule-binding and I came across this error: So while adding dihedral corrections to Martini topology using ./bbsc.sh Protein_A.itp 181L.pdb, the resulting .itp file show the following error being appended to the .itp file: ERROR) BaseMolecule: Cannot bond atom 0 to itself. ERROR) BaseMolecule: Cannot bond atom 0 to itself. ERROR) BaseMolecule: Cannot bond atom 0 to itself. ERROR) BaseMolecule: Cannot bond atom 0 to itself. ERROR) BaseMolecule: Cannot bond atom 0 to itself. ERROR) BaseMolecule: Cannot bond atom 0 to itself. ERROR) BaseMolecule: Cannot bond atom 0 to itself. ERROR) BaseMolecule: Cannot bond atom 0 to itself. ERROR) BaseMolecule: Cannot bond atom 0 to itself. ERROR) BaseMolecule: Cannot bond atom 0 to itself. ERROR) BaseMolecule: Cannot bond atom 0 to itself. moving CA and CB to center of mass of BB, SC1 bead measuring SC BB BB SC dihedrals [ dihedrals ] ; SC-BB-BB-SC dihedrals can't read "rsd": no such variable
On running vmd in my system I get the follwing warnings: /usr/local/lib/vmd/vmd_LINUXAMD64: /usr/lib/x86_64-linux-gnu/libGL.so.1: no version information available (required by /usr/local/lib/vmd/vmd_LINUXAMD64)
followed by
Info) Multithreading available, 8 CPUs detected. Info) CPU features: SSE2 AVX AVX2 FMA Info) Free system memory: 1175MB (14%) Info) No CUDA accelerator devices available. Warning) Detected X11 'Composite' extension: if incorrect display occurs Warning) try disabling this X server option. Most OpenGL drivers Warning) disable stereoscopic display when 'Composite' is enabled. Info) OpenGL renderer: Mesa DRI Intel(R) UHD Graphics 620 (Kabylake GT2) Info) Features: STENCIL MSAA(4) MDE CVA MTX NPOT PP PS GLSL(OVFS) Info) Full GLSL rendering mode is available. Info) Textures: 2-D (16384x16384), 3-D (512x512x512), Multitexture (8) Info) Dynamically loaded 2 plugins in directory: Info) /usr/local/lib/vmd/plugins/LINUXAMD64/molfile
Please help!