AMBER Archive (2009)

Subject: Re: [AMBER] Alpha-L-Methys Fucose structure problem bond 0fA.d.C1 OME.d.O "S"

From: Bill Ross (
Date: Wed Jul 15 2009 - 11:53:41 CDT

> > bond 0fA.d.C1 OME.d.O "S"
> it says
> > bond: Argument #1 is type String must be of type: [atom]
> usage: bond <atom1> <atom2> [order]

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.
Something like

> bond mypdb.1.C1 mypdb.2.O

assuming the residues are the 1st and 2nd in the pdb file.
The 'd' in the pdb file is ignored by loadpdb.

You can 'desc mypdb' to get an idea what is in it and how to address it.


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