Re: [AMBER] creation of disulfide bonds

From: Hannes Loeffler <>
Date: Fri, 8 Nov 2013 10:46:51 +0000

On Fri, 8 Nov 2013 04:18:57 -0600
"Beale, John" <> wrote:

> I am trying to use the "bond" command in xleap to create disulfide
> bonds in a protein. I use the following syntax on the example below:
> bond cyx.117.SG cyx.129.SG
> The bonding fails, and xleap gives me the following error message:
> bond: Argument #1 is type String must be of type: [atom]
> usage: bond <atom 1> <atom 2> [order]
> Other information: the protein possesses two chains, A and B, and a
> few of the disulfide designations are the same in both chains.
> Do I need to specify the chain designation with the "bond" command?
> If so, how do I do this?
> I have followed this procedure successfully many times before. I
> can't figure out what I am doing wrong.

You would need to do this via the variable you use with loadpdb.

p = loadpdb protein.pdb
bond p.117.SG p.129.SG

As far as I am aware of leap doesn't know of chain IDs (a real shame!)
but will simply renumber residues consecutively starting from the first
residue number it finds in the PDB. So it would probably be best to
first write out anoterh PDB first from leap to see what residue numbers
it generates and then adjust the bond commands accordingly.

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Received on Fri Nov 08 2013 - 03:00:03 PST
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