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marrink-lab / vermouth-martinize

Describe and apply transformation on molecular structures and topologies
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adding dihedral correction using martini beta version appends error message to .itp file. #404

Closed majumderS closed 2 years ago

majumderS commented 2 years ago

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!

Tsjerk commented 2 years ago

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.