Are there already some tools available, or we can code for finding the atoms/residues that can contribute the steric clashes before minimization solve the issue?
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2 Answers
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MolProbity
That programs use the Clashscore to account for the number of pairs of atoms in the model that are unusually close to each other. It is expressed as the number or such clashes per thousand atoms.
MolProbity usefull information:
- Oficial site: http://molprobity.biochem.duke.edu/.
- Github repository: https://github.com/rlabduke/MolProbity.
- Reference: Vincent B. Chen, W. Bryan Arendall III, Jeffrey J. Headd, Daniel A. Keedy, Robert M. Immormino, Gary J. Kapral, Laura W. Murray, Jane S. Richardson and David C. Richardson, MolProbity: all-atom structure validation for macromolecular crystallography, Acta Crystallographica Section D, 66 12-21 (2010). DOI: 10.1107/S0907444909042073.
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Using Tcl scripting in VMD
noh and exwithin 0.5 of noh
exwithin is basically the within keyword, but an atom is excluded from its own within list.
Usage:
Load the molecule
set molid [mol load pdb $pdbname]
Make a selection and get the clashing indices.
set clashing_sel [atomselect $molid "noh and exwithin 0.5 of noh"]
set clashing_indices [$clashing_sel get index]
