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Hello Benjamin-- Sorry for the long delay- I've been busy helping with a course here at NIH. > > 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) > > 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? > Do note that the constraints interaction statement only affects a subset of XPLOR potential terms. A description of these terms can be found here http://nmr.cit.nih.gov/xplor-nih/doc/current/xplor/node132.html I suspect this is your problem. best regards-- Charles -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.9 (GNU/Linux) Comment: Processed by Mailcrypt 3.5.8+ <http://mailcrypt.sourceforge.net/> iD8DBQFIrXKdPK2zrJwS/lYRArneAJ41OoZEcnrR5D6u+abjvOmjP8Md/ACfVYNM WZRp8SqEfWhMYtcGz9ijiZc= =pjQs -----END PGP SIGNATURE-----
