pdb2gmx isn't acceptable for any molecule. Only for proteins and DNA-RNA. β-cyclodextrin is present in atb.uq.edu.au in many variants for force field G54A7FF Or it is quit simple to build β-CD with glycan builder and modeller from charrm-gui.org (7 times connect α glucose with 1-4 link). One drawback is that this tool produces linear or branched glycans , but CD is cyclic. You must edit topology and reproduce AGLC residue 7 times (bonds, pairs, angles, dihedrals). If you trust me I can give you my own coordinates and itp for β-CD in oplsaa and charmm36 FF that I use in work. -- Gromacs Users mailing list
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