For example, if I were to load a .pdb or .cif file to Avogadro or VESTA, is there a way to click on the carbon atoms next to oxygen atoms and label them "Ct" so that then when the coordinate data is exported the new tabulated .pdb has those carbon atoms' coordinate information followed by Ct as the label.

This would be pretty helpful for building molecular topologies in gromacs, amber and the like. I thank you in advance, for your attention.

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