Re: [AMBER] non standard residue and bond command

From: Bill Ross <>
Date: Wed, 16 Dec 2009 13:20:08 -0800 (PST)

> 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?


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Received on Wed Dec 16 2009 - 13:30:05 PST
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