dear all, i want to work on two protein-ligand-complexes in the same instance of xplor at the same time. in the segment section i called the protein part of complex 1 PRO1, the ligand LIG1; and PRO2 and LIG2 accordingly (the coordinates of the two proteins partially overlap). after hydrogen adding i want to separate the respective complexes from each other using
CONStraints INTEraction (segid PRO1) (segid PRO1) INTEraction (segid PRO2) (segid PRO2) INTEraction (segid LIG1) (segid LIG1) INTEraction (segid LIG2) (segid LIG2) INTEraction (segid PRO1) (segid LIG1) INTEraction (segid LIG1) (segid PRO1) INTEraction (segid PRO2) (segid LIG2) INTEraction (segid LIG2) (segid PRO2) END then i perform energy minimization and short MD simulation (the random seed i set same for each run). when i compared the coordinate output of this combined runs with two separate runs of the single complexes, i noticed quite big rmsds between the corresponding structures. this might be no surprise due to the fact that i perform energy minimization of the two complexes simultaneously and the way of minimizing the energy of the whole system might be different from minimizing the single systems. i next tested the same setup as described above with the second complex rotated or translated. now the system is the same as above, and if the two complexes do not see each other (as i want them to) the outcome should be the same, which it is not. am i overlooking something really simple? the energy terms i use in the minimization step are bond angle impr vdw elec, maybe there is a term which is excluded from the interaction constraint? or might it be some non-bonded interaction i do not capture with the constraint? best regards, benjamin
