Excellent summary of the RMS situation.
To make comparisons between structures with slightly different
atom numbers, you need to change the crd/rst/pdb file of one to
match the other and use the same prmtop for both in CARNAL. This
can be done by removing atoms with the PTRAJ facility in AMBER.
More recent versions of carnal can also do this via the
use of GROUP with COORD, e.g. in the case of subtracting
a differing residue:
...
DECLARE
GROUP g1 ((SOLUTE) & !(RES 445)) ;
OUTPUT
COORD c1 GROUP g1 ;
END
A prmtop with the residue deleted is also needed.
Ptraj or Rdparm may be able to do this.
Loading a pdb with the residue deleted into Leap and
doing a saveamberparm would work, but there is a chance
that the molecules could be reordered if a TER card
is used in the pdb to break the solute; without the
TER, a false bond would connect the residues adjacent
to the deleted one, which may not be a problem in
carnal except the introduction of some spurious torsions
in TORSION BACKBONE.
Bill Ross
Received on Wed Oct 27 1999 - 11:57:28 PDT
