I experience difficulties when submitting an enzyme PDB file with the
substrates AMP and a non-proteinogenic amino acid to the RosettaDesign webserver.
AMP is well accepted but problems arise with the amino acid substrate.
If I name the amino acid with a common identifier such as PHE in PyMOL, its chemical
structure is changed towards e.g. Phe during the design calculations. If I name it differently such as XYX,
the substrate is discarded in calculations. How should I name the molecule so that
it is kept in enzyme design calculations and not chemically modified during the pipeline?
Thanks in advance!