On Fri, 10 Dec 2010 08:41:14 +0000 imtiaz <biobrain@...> wrote:
> I want to create a Pseudoatom in the center of a benzene ring for a ligand.
> I can easily create a Pseudoatom in the center of aromatic ring of
> amino acids in a protein by following the instructions give at
> load $TUT/1hpv.pdb
> pseudoatom pi_cent,b/53/cg+cz
> However I am not sure how I can do similar thing for the lignad. The
> lignad I have is an indole derivative and I want to create a
> pseudoatom in the center of the 6 member ring of the indole.
If you simple select to of the atoms on opposite sides of the ring (i.e. so
they are called "pk1" and "pk2", then you can do something like this:
pseudoatom indole_centre, pk1|pk2
Robert L. Campbell, Ph.D.
Senior Research Associate/Adjunct Assistant Professor
Botterell Hall Rm 644
Department of Biochemistry, Queen's University,
Kingston, ON K7L 3N6 Canada
Tel: 613-533-6821 Fax: 613-533-2497