[gmx-users] Adding_topology_aminoacid

[shahid nayeem]

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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