Re: [AMBER] Problem with link atom in QM/MM

From: Ross Walker <>
Date: Wed, 16 Mar 2011 09:39:41 -0700

Hi Lee,

Please double check the bonds you expect to be breaking between the QM and
MM region and make sure that you are not breaking 2 bonds to the same atom.
Each QM atom can only have one link atom. I suggest drawing a 2D diagram of
the QM and nearby MM region so you can be sure which bonds you expect to be
broken. Posting this to the AMBER list would be helpful in debugging your

All the best

> -----Original Message-----
> From: Wook Lee []
> Sent: Wednesday, March 16, 2011 8:02 AM
> To:
> Subject: [AMBER] Problem with link atom in QM/MM
> Dear Amber users,
> I got an error message below while I'm running QM/MM MD in Amber11.
> QMMM: ERROR with link atom 1
> QMMM: MM id is: 2476
> QMMM: id of next MM atom is: 2476
> SANDER BOMB in subroutine identify_link_atoms
> Illegal Link Atom Specification.
> either a MM atom has been substituted by more than one link atom or the
> list of MM link pairs is not in numerical order. Cannot continue.
> I think it has something to do with my non standard QM residue because
> when I did QM/MM MD with standard residues, it gave no error message.
> This non standard QM residue is modified cysteine residue where sulfur
> atom is connected to acyl group. (residue name : CYG)
> I include all atoms until CB to QM part so that MM part starts from CA
> atom (This CA is the MM atom with id 2476).
> I would appreciate it if anyone could help me with this problem.
> Cheers,
> Wook
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Received on Wed Mar 16 2011 - 10:00:03 PDT
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