Re: AMBER: bond between two polypeptides

From: David A. Case <>
Date: Tue, 14 Sep 2004 09:20:23 -0700

On Tue, Sep 14, 2004, Jagdish Rai wrote:

> the tleap program refused to make bond between two polypeptides in a PDB
> file which has a TER line next to last atom line of first polypeptide
> bond ss3.10.SG ss3.20.SG
> bond: Argument #2 is type String must be of type: [atom]
> usage: bond <atom1> <atom2> [order]
> but if i remove this TER line it can make a disulfide bond together with

Which version of Amber are you using? In some earlier versions, the residue
numbers for chains after the first one were modified (I think by adding 10000
for each new chain.)

Anyway, use the "desc" command to figure out exactly how tleap is numbering
your system. In your case, if you do "desc ss3.20" will (probably) find
either that this is not a residue, or that it does not contain an atom called
"SG". By typing "desc ss3" you can find out what how all of the residues are

....good luck....dac

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Received on Tue Sep 14 2004 - 17:53:00 PDT
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