AMBER Archive (2009)

Subject: Re: [AMBER] non standard residue and bond command

From: Bill Ross (ross_at_cgl.ucsf.edu)
Date: Wed Dec 16 2009 - 15:20:08 CST

> I load the prepi files first, then the pdb file. I try to use bond
> command and try to connect with single bond between two residues e.g.
> HE1.O60 and HE2.C39 Now as the residues are from two different units,
> the bond command doesnt create a single bond, there are no errors or
> warnings but I simply dont see a bond between two residues when I try
> to save a new pdb file.

When you loadpdb, it's "X = loadpdb <file>". Are you bonding
X.res1.atom to X.res2.atom? (I forget the actual syntax), i.e.
bonding atoms within (units within) X?

Bill

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