[AMBER] Problem with link atom in QM/MM

From: Wook Lee <wlee.chemie.uni-wuerzburg.de>
Date: Wed, 16 Mar 2011 16:01:31 +0100

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.



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Received on Wed Mar 16 2011 - 08:00:10 PDT
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