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Dear all,
I am refining a protein structure which contains a ligand (ADP) in
double conformation. The first conformation occupies entirely the
expected position. In the second one, the two phosphates occupy the same
position as the first one, while the rest of the molecule are clearly
rotate around the O3A and PA bond, filling a different cavity of the
protein.
I've tried to refine with both CNS and Refmac. In the first case, one
of the conformation remains at the right position and the other is
pushed away towards the solvent. I have used the alternate.inp script to
generate the double conformation and select the ligand's atoms as
alternate conformation in the minimize.inp protocol. Refmac are
destroying completely the ligand's geometry, even when I use libraries
created by myself from the ADP coordinates.
Am I missing something? How can I refine this structure? All
suggestions are welcome.
Thank you,
Marcos
