Dear All I am solvating my protein in a cubical box with a .gro file containing water and one amino acidX. when I run grompp I get error "No such moleculetype aminoacidX" . Should I create de novo .itp file for the amino acidX on proDrg because I tried to include ffbonded.itp and ffnonbonded.itp in .top file but this also gives error in grompp. Creating a new .itp file on ProDrg will again cause problem of charge and parametrization. Since it is individual normal amino acid not present in protein but as insert molecule in solvation box so I think creating new .itp file should not be needed. shahid Nayeem
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