Custom Search
-- 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 25, 2013, at 10:41 AM, Alfredo Quevedo wrote: > 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 >>> >>> >>> _______________________________________________ >>> AMBER mailing list >>> AMBER.ambermd.org >>> http://lists.ambermd.org/mailman/listinfo/amber >> >> _______________________________________________ >> AMBER mailing list >> AMBER.ambermd.org >> http://lists.ambermd.org/mailman/listinfo/amber > > > -- > ********************************************************* > 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 > > > _______________________________________________ > AMBER mailing list > AMBER.ambermd.org > http://lists.ambermd.org/mailman/listinfo/amber _______________________________________________ AMBER mailing list AMBER.ambermd.org http://lists.ambermd.org/mailman/listinfo/amberReceived on Thu Jul 25 2013 - 16:30:02 PDT