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 - 08:00:10 PDT
