Author Topic: parameterization of copper ion with four ligand.  (Read 6005 times)

fantastic2012

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parameterization of copper ion with four ligand.
« on: May 23, 2012, 05:36:53 PM »
I am trying to get the parameters of a copper ion with four ligands using QMMM simulations, gromacs interfaced with turbomole (version 6.3).
For the QM method, I choose B3LYP/DFT, I set the control file based on Prof. Ulf Ryde's webpage, and here is my control file after calculation.

$title
calculations of Model2
$operating system unix
$symmetry c1
$redundant    file=coord
$coord    file=coord
$user-defined bonds    file=coord
$atoms
c  1,4,7,10,13,15,19,21,24,26,30,32,35,37,41                                   \
   basis =c def2-TZVP
h  2-3,5-6,11-12,16,18,20,22-23,27,29,31,33-34,38,40,42,44-47                  \
   basis =h def2-TZVP
o  8-9                                                                         \
   basis =o def2-TZVP
n  14,17,25,28,36,39                                                           \
   basis =n def2-TZVP
cu 43                                                                          \
   basis =cu def2-TZVP
$basis    file=basis
$rundimensions
   dim(fock,dens)=520789
   natoms=47
   nshell=360
   nbf(CAO)=1018
   nbf(AO)=896
   dim(trafo[SAO<-->AO/CAO])=1262
   rhfshells=2
$uhfmo_alpha   file=alpha
$uhfmo_beta   file=beta
$uhf
$scfiterlimit       120
$thize     0.10000000E-04
$thime        5
$scfdump
$scfintunit
 unit=30       size=0        file=twoint
$scfdiis
$point_charges file=point_charges
$point_charge_gradients file=point_charge_gradients
$drvopt
   point charges on
   cartesian  on
   basis      off
   global     off
   hessian    on
   dipole     on
   nuclear polarizability
$interconversion  off
   qconv=1.d-7
   maxiter=25
$optimize
   internal   on
   redundant  on
   cartesian  off
   global     off
   basis      off   logarithm
$coordinateupdate
   dqmax=0.3
   interpolate  on
   statistics    5
$forceupdate
   ahlrichs numgeo=0  mingeo=3 maxgeo=4 modus=<g|dq> dynamic fail=0.3
   threig=0.005  reseig=0.005  thrbig=3.0  scale=1.00  damping=0.0
$forceinit on
   diag=default
$energy    file=energy
$grad    file=gradient
$forceapprox    file=forceapprox
$lock off
$dft
   functional b3-lyp
   gridsize   m3
$scfconv   6
$scfdamp   start=0.700  step=0.050  min=0.050
$scforbitalshift  closedshell=.05
$esp_fit kollman
$pointval geo=point pot fmt=xyz

$alpha shells
 a       1-100                                  ( 1 )
$beta shells
 a       1-99                                   ( 1 )
$natural orbitals    file=natural
$natural orbital occupation    file=natural
$actual step      dscf
$statistics  off parallel
$2e-ints_shell_statistics    file=metastase
$last SCF energy change = -2704.6669
$dipole from dscf
  x   -37.89237773743575    y   -11.10930932815100    z   -49.51540742963302    a.u.
   | dipole | =  160.9767574224  debye
$2e-ints'_shell_statistics
  file=metastase
$end

I should get something in the tp.xyz file, but it is empty. If I want to get the ESP of my system, how should I edit my control file? Thanks very much!

Arnim

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Re: parameterization of copper ion with four ligand.
« Reply #1 on: May 24, 2012, 01:35:42 PM »
Hi,

with 'geo=point' you have specified the non-default grid option, but you did not define any grid point.
According to the MANUAL (subtle hint...) it should look like this:
$esp_fit kollman
$pointval geo=point pot fmt=xyz
7 5 3
0 0 7
1 2 3

Cheers,

Arnim