From: Luis Agullo (
Date: Wed Sep 10 2014 - 14:49:13 CDT

In several frames of a dynamics (NAMD) one of the segments of a dimer
gets out of the box. I thought that this situation would not affect the
calculation of energies of interaction between the two monomers, but I
obtain results that do not seem reasonable in those frames. Then, I have
tried to put both segments of the dimer together in the same box
following the indications published in other posts of this list, as for
instance the commands:

1) << pbc wrap all -centersel protein -center com -compound res >> [the
'standard'] --> WITHOUT SUCCESS

or 2) pbc wrap -all -centersel "serial 463 482 501 736 746 767 2203 2219
2220 2233 2257 2274 2391" -center com -compound chain >> [trying to
center the box in atoms of monomer 1 and 2 close to the surface of
interaction and trying to avoid the separation of the monomers that
belongs to the same chain -different segments-] --> WITHOUT SUCCESS

or 3) <<pbc set {65.622 95.458 72.223} -all >> and then << pbc wrap
-center bb -centersel protein -compound res -all >> --> WITHOUT SUCCESS

or 4) << pbc join chain -ref "serial 1425 2219" >> [trying to force
atoms of the same chain, but of different segment, to remain together
and centered in those atoms of the interphase] --> I obtain the error
'expected integer but got "P"' !!!??? [the identity of the chain is "P",
but it is normal, isn it?]

or many other similar approaches...

I supposed that I miss something, because it seems to be a frequent
problem in dynamics.