Issue with preparing QM-MM

From: Francesco Pietra (
Date: Thu Feb 27 2020 - 12:32:58 CST


My question is whether there is a way to circumvent the inability of
<prepare.qm.region.tcl> (vmd text mode) with nucleotides and a small
organic ligand, to recognize residue number 0 for the organic ligand

set seltext "(nucleic and resid 0 3 5 7 8 9)"

the generated .QMonly.psf contains all except what relates to resid 0.
I understand that I could renumber the starting pdb and rebuild psf/pdb,
but I have already equilibrated the system with resid 0. Segname is not
useful here because it does not discriminate the nucleotides.

Thanks for advice
francesco pietra

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