merc mertens wrote:
hello,
i have got a problem with my simulation setup. i prepare a protein with two ligands in a
dodecahedral box. after the setup the ligands are situated in the active site of the
protein all right. when i look at the structure after em one of the ligands is now
outside the protein in the solvent. if i generate symmetry mates the ligand is perfectly
at its typical position in the active site of the next symmetry related molecule. yet the
flag "-pbc nojump" in trjconv does not produce a whole molecule!! therefore it
seems that the ligand is translated during the em step. when i look at the structure
before em i see that the ligand is outside the solventbox (but inside the dodecahedral
box!!!) and translated inside the solventbox after em. unfortunately i have no idea how
to solve this problem except to make the box so huge, that calculation becomes too time
consuming, as the protein is a tetramer with nearly 1500 residues.
Have you tried the trjconv option that puts the COM of each molecule (or
residue, I forget) inside the box?
Mark
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