Dear Abhishek,
The QM/MM interface to external QM programs works as described in the manual. As an example you can also look at the tests in $AMBERHOME/test/qmmm_EXTERN/.
The input file that you describe does not have a valid entry for the &qmmm namelist variable iqmatoms. It should be a comma separated list of integers.
If you have not yet resolved your problems, you can send me your input files (mdin, prmtop, inpcrd) off list and I can check what is wrong.
All the best,
Andy
—
Dr. Andreas W. Goetz
Assistant Research Scientist
San Diego Supercomputer Center
Tel: +1-858-822-4771
Email: agoetz.sdsc.edu
Web: www.awgoetz.de
> On Jan 10, 2018, at 10:02 AM, Thakur, Abhishek <axt651.miami.edu> wrote:
>
> But I want to use B3LYP via gaussian for QM.
>
> ________________________________
> From: Marcelo Andrade Chagas <andrade.mchagas.gmail.com>
> Sent: Wednesday, January 10, 2018 6:43:58 AM
> To: AMBER Mailing List
> Subject: Re: [AMBER] QM/MM MD B3LYP
>
> Dear,
>
> QM / MM - MD already programmed in AMBER using DFT for part QM?
>
> Best regards
>
> Marcelo Andrade Chagas, MSc
> (PhD student)
> Laboratório de Química Computacional e Modelagem Molecular - LQC-MM
> * https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Flqcmm.qui.ufmg.br%2F&data=02%7C01%7Caxt651%40miami.edu%7Ca43bcafd8b0842fc0df608d55851c612%7C2a144b72f23942d48c0e6f0f17c48e33%7C0%7C0%7C636512030596901206&sdata=AghFgJGRAopYIBroU9e81gSRFKYe1TAO1Mu1BbnXP9c%3D&reserved=0
> Departamento de Química da Universidade Federal de Minas Gerais - UFMG
> Tel:(31)3409-5776
>
> 2018-01-10 15:35 GMT-02:00 Thakur, Abhishek <axt651.miami.edu>:
>
>> Hi everyone,
>>
>> I am using a script for QM/MM/MD minimization but getting convergence
>> problem
>> Convergence failure -- run terminated.
>>
>>
>> cat > mdin << EOF
>> Minimization of B4M_QM_MM all atoms
>> &cntrl
>> imin=1, maxcyc=1000,
>> ntc=1, ntf=1, ntb=1, ntpr=5,
>> ifqnt=1
>> /
>> &qmmm
>> iqmatoms= ****
>> qmcharge=0,
>> qm_theory='EXTERN',
>> qmshake=0,
>> spin=1,
>> qm_ewald=0, qm_pme=0,
>> diag_routine=0,
>> writepdb=1
>> /
>> &gau
>> mem = ‘25GB’
>> method = ‘B3LYP’,
>> basis = ‘6-31G**‘,
>> num_threads = 16,
>> use_template = 0,
>> /
>> EOF
>>
>>
>>
>>
>> If I use use_template = 1, then my minimization crashes but it works well
>> with use_template = 0,
>>
>>
>>
>> Another question that I have is
>>
>> As in my script I have given
>>
>>
>> mem = ‘25GB’
>> method = ‘B3LYP’,
>> basis = ‘6-31G**‘,
>>
>> but amber greates a gau_job.inp which has
>> %chk=gau_job.chk
>> %NProcShared=16
>> %mem=256MB
>> #P BLYP/6-31G* SCF=(Conver=8) NoSymm Force Charge Prop=(Field,Read)
>>
>> I have mentioned 25GB in my script still it is using 256MB and basis that
>> I have given is 6-31G** but I can see it is applying 6-31G*
>>
>>
>> Moreover if I want to tell amber to use something else rather than
>>
>>
>> #P BLYP/6-31G* SCF=(Conver=8) NoSymm Force Charge Prop=(Field,Read)
>>
>>
>> How do I tell it and make certain changes in my script.
>>
>>
>> I will really appreciate any suggestion.
>>
>> Thanking you,
>> -ABhishek
>>
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>>
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Received on Wed Jan 10 2018 - 21:30:03 PST
