Dear Ross
I have checked several times with VMD and looked into pdb file whether
this boundary QM atom has more than one link atom
because I also suspected what you said.
However, this QM atom should have only one link atom as I checked.
Cheers,
Wook
On 03/16/2011 05:39 PM, Ross Walker wrote:
> 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
> problem.
>
> All the best
> Ross
>
>
>> -----Original Message-----
>> From: Wook Lee [mailto:wlee.chemie.uni-wuerzburg.de]
>> Sent: Wednesday, March 16, 2011 8:02 AM
>> To: amber.ambermd.org
>> 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 Thu Mar 17 2011 - 02:00:02 PDT
