Thank Gustavo for replying.
I moved on, basically the Li+ atoms were included in "file.mol2", and it
didn't work.
But now I let AMBER add Li+ around the molecule " addIons2 mol LI 27" , so
that my the topology file had charge 24+ ( because the molecule has charge
3-). And , using adjust_q=2, the system is now neutralized and the
calculation is running fine.
However, I am using AMBER(serial) with ORCA( 24-CPUs) and it is really
slow? Do you have any idea how to get it faster?
I am treating the molecule at QM , and the Li at MM. Here is my "file.in"
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,
writepdb=1,
adjust_q=2,
qm_ewald=0, qm_pme=1
/
&orc
use_template=1
/
Best regards,
Emanuele
2018-07-31 13:12 GMT+01:00 Gustavo Seabra <gustavo.seabra.gmail.com>:
> Hi,
>
>
>
>
> 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.
>
>
>
>
> HTH,
>
>
> --
>
>
> 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 _______________________________________________
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Received on Thu Aug 02 2018 - 08:00:02 PDT
