have tried that too Dr.Roitberg but it does not work.
Here is my script
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=2077,2078,2079,2080,2081,2082,2083,2084,2085,2086,2087,2088,2089,2090,2091,5310,5311,5312,5313,5314,5315,5316,5317,5318,5319,5320,5321,5322,5323,5324,5325,5326,5327,5328,5329,5330,5331,5332,5333,5334,5335,5336,5337,5338,5339,5340,5341,5342,5343,5344,5345,5346,5347,5348,5349,5350,5351,5352,5353,5354,5355,5356,5357,5358,5389,5390,5391,5392,5393,5394,5395,5396,5397,5398,5399,5400,5401,5402,5403,5404,5405,5406,5407,5408,5409,5410,5411,5412,
qmcharge=0,
qm_theory='EXTERN',
qmshake=0,
spin=1,
qmcut=99999
diag_routine=0,
writepdb=1
&end
&gau
method = ’B3LYP’,
basis = ’6-31G**’,
mem = ‘25GB’,
num_threads = 8,
use_template=1,
&end
EOF
________________________________
From: Adrian Roitberg <roitberg.ufl.edu>
Sent: Tuesday, January 9, 2018 5:54:21 AM
To: Thakur, Abhishek
Subject: Re: [AMBER] qm2_extern_gau_module
amber16 manual, page 158
&gau
method = ’BP86’,
basis = ’6-31G**’,
num_threads = 8,
mem=’1GB’,
/
not !method like you have
can you check?
adrian
On 1/9/18 11:49 AM, Thakur, Abhishek wrote:
> Thank you Dr.David, I was working on your suggestion and could solve up to great extent. But I am confused at one place, As I am seeing the output file I can see it is using PM3 but I am using
> !method=‘B3LYP’,
> !basis=‘6-31G**’,
> I am not sure what is happening.
>
>
> 3.1 QM CALCULATION INFO
> --------------------------------------------------------------------------------
>
> | QMMM: Citation for AMBER QMMM Run:
> | QMMM: R.C. Walker, M.F. Crowley and D.A. Case, J. COMP. CHEM. 29:1019, 2008
>
> QMMM: SINGLET STATE CALCULATION
> QMMM: RHF CALCULATION, NO. OF DOUBLY OCCUPIED LEVELS =132
>
> | QMMM: *** Selected Hamiltonian ***
> | QMMM: PM3
>
>
>
>
> ________________________________
> From: David Poole <thepoole.ucdavis.edu>
> Sent: Saturday, January 6, 2018 11:48:40 AM
> To: amber.ambermd.org
> Subject: Re: [AMBER] qm2_extern_gau_module
>
> Hello Thakur,
>
> I really hate double posting, but sometimes I get to learn google keyboard
> shortcuts. That said..
> You shouldn't need to specify your version of Gaussian, the module will
> check which version is in your path for you. I believe everyone else is
> saying this.
> If you are having problems with the method of basis, I'd really suggest
> using your own template file (this is well documented). It allows a greater
> flexibility in your calculations, e.q. using quadratic convergence for the
> self-consistent field.
>
>
> On a related suggestion, I had encountered some errors when running Amber
> 14 with QMMD using the qm2_extern module, this has to do with the formchk
> utility behaving differently than expected. To get it to work, I modified
> the conditional at line 157 of the Fortran code to ignore the return value.
> However, in the end I found g09 rev D was more efficient to use with Amber
> and would suggest you the same.
>
> Here is a complete input file for doing QMMD that I use, carefully review
> the gau and qmmm portions and look up what each parameter does and how you
> need to modify it for your use case.
> &cntrl
> imin=0, ntb=0, ig=-1, irest=0,
> cut=9999.0,
> tempi=0.0, temp0=350,
> ntt = 3, gamma_ln = 5.0,
> ifqnt=1,
> nstlim=2500, dt=0.001,
> ntpr=1, ntwx=1, ntwf=1, ifqnt=1
> &end
> &qmmm
> qmmask='*',
> spin=1,
> qmcharge=-2,
> qm_theory='EXTERN',
> qmcut=99999
> &end
> &gau
> num_threads=16,
> mem=25GB,
> use_template=1
> &end
>
> Note that I am using a template, this is just the route section of a
> gaussian input file, e.g.
> # ub3lyp/def2SVP integral=grid=ultraf1ine scf=qc
>
>
> That said, good luck and tot zeins.
>
> -David
>
> On 6 January 2018 at 23:42, David Poole <thepoole.ucdavis.edu> wrote:
>
>> Hello Thakur,
>>
>> You shouldn't need to specify your version of Gaussian, the module will
>> check which version is in your path for you. I believe everyone else is
>> saying this.
>>
>> If you are having problems with the method of basis, I'd really suggest
>> using your own template file (this is well documented). It allows a greater
>> flexibility in your calculations, e.q. using quadratic convergence for the
>> self-consistent field.
>>
>> Also, I have encountered some errors when running Amber 14 with QMMD using
>> the qm2_extern module, this has to do with the formchk utility behaving
>> differently than expected. For better or worse I'd modified the module to
>> simply ignore the return value of formchk.
>>
>> Here is a complete input file for doing QMMD
>> &cntrl
>> imin=0, ntb=0, ig=-1, irest=0,
>> cut=9999.0,
>> tempi=0.0, temp0=350,
>> ntt = 3, gamma_ln = 5.0,
>> ifqnt=1,
>> nstlim=2500, dt=0.001,
>> ntpr=1, ntwx=1, ntwf=1, ifqnt=1
>> &end
>> &qmmm
>> qmmask='10',
>> qmcharge=-2,
>>
>> qm_theory='EXTERN',
>> qmcut=99999
>> &end
>> &gau
>> num_threads=16,
>> mem=25GB,
>> use_template=1
>> &end
>>
>> Note to change the
>>
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--
Dr. Adrian E. Roitberg
University of Florida Research Foundation Professor
Department of Chemistry
University of Florida
roitberg.ufl.edu
352-392-6972
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Received on Tue Jan 09 2018 - 09:30:02 PST
