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Dear All ,
In order to determine the interaction between a magnesium atom from chlorophyll and a gluamate atom, I performed my QM calculations for geometry scan.I completed my QM calculations for the geometry scan, but here are some specifics:
to go further in QMMM approch using Gromacs, there are also one protein isoleucine connected with glutamate and phytol tail , which belong to chlorophyll , the previously mentioned parts were removed from QM calculations just to reduce the computationals effort and cost.
Now my question how to add the isoleucine and phytol tail using the best software ?
I tried to add them manually using avogadro but unfortunately I did not get any success.