# Re: [AMBER] QM/MM using Gaussian03 as External

From: Alfredo Quevedo <alfredoq.fcq.unc.edu.ar>
Date: Thu, 25 Jul 2013 14:41:56 -0300

Dear Andreas, thank you very much for your feedback. As you point out I
was expecting that the keyword "Punch=Derivatives" in the route section
of gaussian may wirte the information required by sander to continue
with the QM/MM calculation. The problem is that the file 'fort.7' is
created by gaussian03 but it is empty although the gaussian job end
without problem. To test this I used the example provided with Amber12
under the test directory.

The input to sander for the QM/MM simulation is:

Geometry optimization with Gaussian, 2 steps steepest descent
&cntrl
imin=1, ! do a minimization
maxcyc=2, ! max 2 minimization steps
ncyc=2 , ! switch to conjugate gradient after 2 steps of steepest
descent
drms=0.5, ! RMS gradient convergence criterium 0.5 (kcal/mol)/A =
2.d-3 au
cut=9999.0, ! non-bonded cutoff (irrelevant for now with pure QM)
ntb=0, ! no periodic boundary conditions
ntpr=1, ! print every minimization step
ntwx=1, ! write coordinates each step
ntwr=2, ! write restart file at last step
ioutfm = 1, ! NetCDF MDCRD.
ifqnt=1 ! do QM/MM
/
&qmmm
qmmask ='.*',
qmcharge = 0,
qm_theory ='EXTERN',
verbosity = 0,
/
&gau
basis = 'STO-3G',
method = 'BLYP',
charge = 0,
/

The input to Gaussian03 as created by sander is:

%chk=gau_job.chk
%NProcShared=1
#P BLYP/STO-3G SCF=(Conver=8) Force Punch=Derivatives NoSymm

Gaussian run using SANDER external interface.

0 1
O 0.0000000000000000 0.0000000000000000 0.0000000000000000
H 1.5000000000000000 0.0000000000000000 0.0000000000000000
H 0.0000000000000000 1.5000000000000000 0.0000000000000000

The .inpcrd and .prmtop files I used are 'h2o.inpcrd' and 'h2o.prmtop',
respectively, under \$AMBERHOME//test/qmmm_EXTERN/pure_QM_MD_GAUSSIAN

As can be seen, the 'Punch=Derivative' keyword is present, and although
the Gaussian calculation ends up OK, charges are not dumped to fort.7.

Which may be causing this situation?

Thank you very much in advance,

Kind regards

Alfredo

El 24/07/2013 17:58, Andreas Goetz escribió:
> Hi Alfredo,
>
> According to the Gaussian03 manual, the file fort.7 should be written if the input file contains "Punch=Derivatives" in the route section (which is the case for input generated by the QM/MM interface in sander). I am almost sure this was tested at some point but do not have access to Gaussian03 to verify.
>
> All the best,
> Andy
>
> --
> Dr. Andreas W. Goetz
> Assistant Project Scientist
> San Diego Supercomputer Center
> Tel : +1-858-822-4771
> Email: agoetz.sdsc.edu
> Web : www.awgoetz.de
>
> On Jul 24, 2013, at 8:07 AM, Alfredo Quevedo wrote:
>
>> Good morning: I am trying to run a test QM/MM simulation using
>> Gaussian03 as external software. The simulation does not finishes
>> because the file fort.7 is not being created. Searching in the amber
>> archive I found the following related thread:
>>
>> http://archive.ambermd.org/201205/0437.html
>>
>> in which the same problem was reported. The reported solution was to use
>> Gaussian09 instead of Gaussian03.
>> My question is: has anyone succeded in running QM/MM simulations using
>> Gaussian03?. In that case, how may the problem related to fort.7 file
>> be fixed?
>>
>> Thank you very much in advance for the help,
>>
>> kind regards
>>
>> Alfredo
>>
>> --
>> *********************************************************
>> Prof. Dr. Mario Alfredo Quevedo.-
>> Laboratorio de Química Medicinal.-
>> Dpto. de Farmacia - Fac. de Ciencias Químicas.-
>> Universidad Nacional Córdoba.-
>> 5000 Córdoba, Argentina
>> TE: +54 351 5353865 Int: 53355
>>
>>
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>
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```--
*********************************************************
Prof. Dr. Mario Alfredo Quevedo.-
Laboratorio de Química Medicinal.-
Dpto. de Farmacia - Fac. de Ciencias Químicas.-
Universidad Nacional Córdoba.-
5000 Córdoba, Argentina
TE: +54 351 5353865 Int: 53355
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Received on Thu Jul 25 2013 - 11:00:02 PDT
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