Re: [AMBER] QM/MM link atoms

From: Gustavo Seabra <>
Date: Tue, 31 Jul 2018 12:12:16 +0000 (UTC)


AFAIK, Sander will only add link atoms in places where it needs to break a bond between QM and MM regions. Also, this 'bond'  must be defined in the prmtop file, i.e., it must be a real bond in your system.

If you only added Li+ íons around the molecule as counterions, there should not be a bond defined, and no link atoms added.

Also, notice that using Sander will *not* help with the charge problem. The QM part is sent to the QM program 'as is' (apart from any link atoms), and if it is highly charged, it will keep this charge in the QM program. Remember that the Li+ íons will be passed only as point charges that do not affect the molecule charge.

The message you are getting actually tells me that the definition of the QM zone may not be getting what you intend, as apparently there remains no MM atoms. Are the Li+ íons being passed as part of the QM zone? From what I understand, they should *not* be included in the mask.

My suggestion is that you try to print the QM region and compare to what you expect. There is a keyword, I believe it it something like 'qmmm_writepdb' (or something like it, check the manual) that tells Sander to write a pdb' file with the QM zone. It will include only the QM atoms (plus any link atoms), but *not* the MM part. With that you can be certain of what is going on.


Gustavo Seabra
De: emanuele falbo
Enviado: terça-feira, 31 de julho 08:09
Assunto: [AMBER] QM/MM link atoms
Para: AMBER Mailing List
Dear admins, I am running a QM/MM simulation interfacing AMBER to ORCA. My system is composed by a molecule, treated at QM level and surrounded by Li+ atoms, which I wish to treat at MM level. The problem is that SANDER keeps saying me that adjust_q=2 requires natom-(nquant+nlink)>=1 . 1. I did not specify to include link atoms, cause I don't know how to do it. " 300K constant temp QMMMMD &cntrl imin=0, ntb=1 cut=8.0, ntc=2, ntf=2, tempi=300.0, temp0=300.0, ntt=3, gamma_ln=1.0, nstlim=1000, dt=0.002, ntpr=1, ntwx=1,ifqnt=1 / &qmmm qmmask='@1-53', qmcharge=0, spin=2, qm_theory='EXTERN', ! Use external QM program qmshake=1, qm_ewald=0, qm_pme=1 / &orc use_template=1 / " 2. This is must be because the charge in file.prmtop is 24- but I used "qmcharge=0" ( because I want ORCA to run a a calculation on a neutral system). 3. In fact, in creating the file.prmtop for my molecule I used the Mulliken charges from an ORCA calculation, and the total molecule charge is 3- . But, I want to surround it by 27 Li+ , and for this reason the total charge will obviously be 24-. The thing is that I can't get the Mulliken charge from ORCA for my molecule, because the molecule 27- doesn't converge, reason why I am trying a QM/MM run to distribute the Li around. Do you have any idea about how this problem can be fixed ? Best Regards, Emanuele _______________________________________________ AMBER mailing list 
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Received on Tue Jul 31 2018 - 05:30:03 PDT
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