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Example: Incorporation of Disulfide Bridges
All protein force fields have the DISU patch residue defined.
To make a disulfide bridge, one should use the patch statement; e.g.,
topology presidue DISU group modify atom 1CB charge= 0.19 END modify atom 1SG type=S charge=-0.19 END group modify atom 2CB charge= 0.19 END modify atom 2SG type=S charge=-0.19 END add bond 1SG 2SG add angle 1CB 1SG 2SG add angle 1SG 2SG 2CB add dihedral 1CA 1CB 1SG 2SG add dihedral 1CB 1SG 2SG 2CB add dihedral 1SG 2SG 2CB 2CA end end patch reference=1=( resid 15 ) reference=2=( resid 25 ) endwill make a disulfide bridge between residue number 15 and residue number 25. (For completeness, the definition of the patch residue DISU is listed here as well. Normally, this patch residue is already included in the topology files.)
Xplor-NIH 2024-09-13