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Mod:Hunt Research Group/Jan data

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Getting data for Jan's Charge analysis code

Files desired

  1. first obtain an optimised geometry, confirm with frequency analysis: file_opt.log file_freq.log
  2. generate charges and mesh: file_ch.log file_nbo.log file_chelpg.log
  3. generate density and ESP cubes: file_dens.cub file_esp.cub

Charges & Mesh

  • generate mk, chelpg and nbo charges by creating sequential files with the keyword pop=mk, pop=nbo and then pop=chelpg
  • also with each file we want to obtain the mesh used by the population analysis method
  • the esp generated by cubegen will be the same irrespective of which pop analysis method you use
  • Antechamber is a set of auxiliary programs in AMBER code "http://ambermd.org/antechamber/ac.html" which can do this
  • we give gaussian an IOP command to generate the antichamber file which contains the esp (and some other data):
  • add "iop(6/50=1)" in the command line
  • at the end of the input file add the filename you want to use for the antichamber file, ie filename.esp
  • for example:
[tricia@dyn1245-162]/Users/tricia/bin/repESP/data/ch3oh $ cat ch3oh_mk.com
%mem=3GB
%chk=ch3oh_mk.chk
# b3lyp/6-311g(d,p) pop=mk geom=connectivity iop(6/50=1)

Title Card Required

0 1
 C                  0.66362500   -0.01956500    0.00000200
 H                  1.08294200    0.98750600   -0.00068100
 H                  1.03512900   -0.54274000   -0.89175700
 H                  1.03523100   -0.54158500    0.89239900
 O                 -0.75011200    0.12170300    0.00000200
 H                 -1.13415200   -0.75941100    0.00001500

 1 2 1.0 3 1.0 4 1.0 5 1.0
 2
 3
 4
 5 6 1.0
 6

ch3oh_mk.esp

[tricia@dyn1245-162]/Users/tricia/bin/repESP/data/ch3oh
  • The log file created ch3oh_mk.log will show the MK charges
...
     419 points will be used for fitting atomic charges
 Fitting point charges to electrostatic potential
 Charges from ESP fit, RMS=   0.00208 RRMS=   0.13573:
 ESP charges:
               1
     1  C    0.174709
     2  H    0.056552
     3  H   -0.008412
     4  H   -0.008391
     5  O   -0.605637
     6  H    0.391179
 Sum of ESP charges =   0.00000
 ESP charges with hydrogens summed into heavy atoms:
               1
     1  C    0.214458
     5  O   -0.214458
 Charge=   0.00000 Dipole=     0.8186    -1.4853    -0.0001 Tot=     1.6960
 Writing Antechamber ESP formatted file "ch3oh_mk.esp"
  • and the ch3oh_mk.esp looks like this at the beginning, this file produces the fitting points and charges used for each method, so in this case we have generated the fitting points and potential determined by the MK charge scheme
 ESP FILE - ATOMIC UNITS
 CHARGE =   0 - MULTIPLICITY =   1
 ATOMIC COORDINATES AND ESP CHARGES. #ATOMS =        6
  C       0.12540691D+01 -0.36972614D-01  0.33595131D-05  0.17470936D+00
  H       0.20464629D+01  0.18661160D+01 -0.12873234D-02  0.56552087D-01
  H       0.19561101D+01 -0.10256299D+01 -0.16851769D+01 -0.84121840D-02
  H       0.19563029D+01 -0.10234473D+01  0.16863893D+01 -0.83910773D-02
  O      -0.14175067D+01  0.22998458D+00  0.33595131D-05 -0.60563743D+00
  H      -0.21432367D+01 -0.14350797D+01  0.27925953D-04  0.39117925D+00
 DIPOLE MOMENT:
 X=  0.31460748D+00 Y= -0.59585599D+00 Z= -0.33506377D-04 Total=  0.67381171D+00
 TRACELESS QUADRUPOLE MOMENT:
   XX=  0.83884443D-01   YY=  0.52009600D+00   ZZ= -0.60398044D+00
   XY=  0.16484276D+01   XZ= -0.12577149D-03   YZ= -0.62668660D-04
 ESP VALUES AND GRID POINT COORDINATES. #POINTS =     419
 -0.56363375D-03  0.22461753D+01  0.16814058D+01  0.34367601D+01
 -0.15112983D-01  0.26196287D+00  0.16814058D+01  0.34367601D+01
  0.11647111D-01  0.52224939D+01 -0.36972614D-01  0.33595131D-05
  0.14811072D-01  0.17324098D+01 -0.39764632D+01  0.33595131D-05
  0.11489694D-01  0.35083914D+01 -0.33029222D+01  0.33595131D-05
  0.12227439D-01  0.47679348D+01 -0.18811916D+01  0.33595131D-05
 -0.56258765D-03  0.22461753D+01  0.16814058D+01 -0.34367534D+01
 -0.15112230D-01  0.26196287D+00  0.16814058D+01 -0.34367534D+01
  0.55425933D-02  0.39125282D+01  0.18661160D+01  0.25671312D+01
  • and the ch3oh_chelpg_esp.cub and ch3oh_mk_cub are identical
Title Card Required potential=scf
 Electrostatic potential from Total SCF Density
    6   -6.388242   -6.549725   -6.512748    1
   85    0.169514    0.000000    0.000000
   78    0.000000    0.169514    0.000000
   78    0.000000    0.000000    0.169514
    6    6.000000    1.254070   -0.036972    0.000004
    1    1.000000    2.046464    1.866116   -0.001287
    1    1.000000    1.956110   -1.025630   -1.685177
    1    1.000000    1.956303   -1.023447    1.686390
    8    8.000000   -1.417506    0.229985    0.000004
    1    1.000000   -2.143237   -1.435079    0.000028
  2.53070E-03  2.64232E-03  2.75842E-03  2.87905E-03  3.00425E-03  3.13404E-03
  3.26840E-03  3.40729E-03  3.55063E-03  3.69832E-03  3.85021E-03  4.00608E-03

Density & ESP

  • generate the density and true ESP (from any run) since these depend only on the electronic structure
  • format the checkpoint files, generate the density and then esp cube files:
formchk file.chk file.fck
cubegen 1 Density=SCF ch3oh.fchk ch3oh_den.cub -2
cubegen 1 Potential=SCF ch3oh.fchk ch3oh_esp.cub -2
  • the results should look something like this
[tricia@orris]/Users/tricia/bin/repESP/data/ch3oh $ ls
ch3oh_mk.chk  ch3oh_mk.com  ch3oh_mk.esp  ch3oh_mk.log  ch3oh_nbo.com ch3oh_nbo.log
[tricia@orris]/Users/tricia/bin/repESP/data/ch3oh $ formchk ch3oh_mk.chk ch3oh.fchk
 Read checkpoint file ch3oh_mk.chk
 Write formatted file ch3oh.fchk
 FChkPn:  Initial coordinates match /B/.
[tricia@orris]/Users/tricia/bin/repESP/data/ch3oh $ 

[tricia@orris]/Users/tricia/bin/repESP/data/ch3oh $ cubegen 1 density=scf ch3oh.fchk ch3oh_dens.cub -2
 Top CubeGen          Tue Mar 27 06:26:29 2018
 Aft UFChkP           Tue Mar 27 06:26:29 2018        0.30 cpu,        0.30 elapsed
 Aft DecCub           Tue Mar 27 06:26:29 2018        0.03 cpu,        0.04 elapsed
 Aft Density          Tue Mar 27 06:26:29 2018        0.00 cpu,        0.01 elapsed
 Bef DoCube           Tue Mar 27 06:26:29 2018        0.00 cpu,        0.02 elapsed
 There are a total of       68800 grid points.
 ElSum from          density=       13.9664751524
 Aft DoCube           Tue Mar 27 06:26:30 2018        0.25 cpu,        0.33 elapsed
[tricia@orris]/Users/tricia/bin/repESP/data/ch3oh $ cubegen 1 potential=scf ch3oh.fchk ch3oh_esp.cub -2
 Top CubeGen          Tue Mar 27 06:26:58 2018
 Aft UFChkP           Tue Mar 27 06:26:58 2018        0.29 cpu,        0.30 elapsed
 Aft DecCub           Tue Mar 27 06:26:58 2018        0.00 cpu,        0.01 elapsed
 Aft Density          Tue Mar 27 06:26:58 2018        0.00 cpu,        0.00 elapsed
 Bef DoCube           Tue Mar 27 06:26:58 2018        0.00 cpu,        0.00 elapsed
 There are a total of       68800 grid points.
 ElSum from          density=       17.1381471886
 Aft DoCube           Tue Mar 27 06:26:59 2018        1.26 cpu,        1.32 elapsed
[tricia@orris]/Users/tricia/bin/repESP/data/ch3oh $
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