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Here you can find some parameters and topology definitions for nonstandard molecules.

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Topology

ArachidonicAcidTop: topopolgy definitions for arachidonic acid (CHARMM format)

PalmitoylCysteinTop: topopolgy definitions for palmitoyl-cystein (CHARMM format)

RetinalTop: topopolgy definitions for retinal bound via protonated Schiff-base link to lysine. Used in rhodopsin. (CHARMM format)

Parameters

ArachidonicAcidPar: parameters for arachidonic acid (CHARMM format)

PalmitoylCysteinPar: parameters for palmitoyl-cystein (CHARMM format)

RetinalPar: parameters for retinal bound via protonated Schiff-base link to lysine. Used in rhodopsin. (CHARMM format)