AMBER Archive (2009)
Subject: Re: [AMBER] Alpha-L-Methys Fucose structure problem bond 0fA.d.C1 OME.d.O "S"
From: Bill Ross (ross_at_cgl.ucsf.edu)
> > bond 0fA.d.C1 OME.d.O "S"
When you loaded the pdb, you created a new unit, e.g. mypdb:
> mypdb = loadpdb my.pdb
So to create a bond within it, you need to name the atoms properly.
> bond mypdb.1.C1 mypdb.2.O
assuming the residues are the 1st and 2nd in the pdb file.
You can 'desc mypdb' to get an idea what is in it and how to address it.