if I want to calculate ESP charge with antechamber, do i just need type the
following command?
~/software/amber12/AmberTools/bin/antechamber -i ../CEP-121G-P.log -fi
gout -o KEG.mol2 -fo mol2 -c esp -nc -3 -s 0
where CEP-121G-P.log is the gaussian log file. if I want to calculate the
mulliken charge, do I just need replace esp with
mul?
I try these ways, and antechamber crash. Am I doing anything wrong? Thank
you~
yours
Bob
2015-10-15 2:17 GMT+08:00 li he <parachuternewyork.gmail.com>:
> Dear amber developers and users,
> I am trying to reproduce PW12O40(3-)'s resp charge in the supplementary
> infomation of the 2008 jpcb paper, "Molecular Dynamics Simulations of
> Dendrimer-Encapsulated r-Keggin Ions in Trichloromethane Solution". I
> follow their quantum chem procedure (the description is in the end of this
> email): B3LYP+SBKJC basis set, and my gaussian input file reads:
>
> %Mem=4GB
> %nprocshared=24
> %chk=test.chk
> #P B3LYP/Gen Integral=Ultrafine Pseudo=Read
> SCF(Conver=8,XQC,MaxConventionalCycles=64,MaxCycle=128) Symm=loose
> 5D 7F Pop=(chelpg,ReadRadii,Regular) IOp(6/33=2) GFinput GFprint
>
> MEP step
>
> -3 1
> P -0.003 -0.000 29.997
> O 0.631 1.267 30.631
> ...
>
> O -0.140 -5.285 29.860
>
> P O W 0
> CEP-121G
> ****
>
> P O W 0
> CEP-121G
> W 1.8
>
> After gaussian calculation is done, I use antechamber:
> ~/software/amber12/AmberTools/bin/antechamber -i ../CEP-121G-P.log -fi
> gout -o KEG.mol2 -fo mol2 -c resp -nc -3 -s 0
>
> My electronic energy from gaussian is -1461.3 a.u., agreeing with theirs
> -1462.4 a.u. but my resp charge looks strange:
> 1 P1 -0.0090 0.0090 0.0000 p5 1 MOL 4.362211
> 2 O1 0.6240 -0.6260 1.2670 o 1 MOL
> -1.703139
> 3 O2 0.2560 1.5370 0.0000 o 1 MOL
> -1.703139
> 4 O3 -1.5380 -0.2520 0.0000 o 1 MOL
> -1.703139
> 5 O4 0.6240 -0.6260 -1.2670 o 1 MOL
> -1.703139
> 6 W1 0.0590 -0.0590 3.5980 W 1 MOL
> 1.785263
> ......
> 17 W12 0.0590 -0.0590 -3.5980 W 1 MOL
> 1.785263
> 18 O5 0.0890 1.7440 2.9340 os 1 MOL
> -0.610356
> ......
> basically, my resp charges for the center PO4 are 4.36 (P) and -1.70 (O),
> for W are 1.79, and for the other 36 oxygens are -0.61. However, their resp
> charges for the 12 outermost O are ~-0.4, and for other else atoms are
> close to 0. I am wondering why my resp charges are so different? Am I doing
> anything wrong?
> I also try 6-311G(d) for P or O atoms: it does not affect resp charge
> much, but lead to electronic energy of about -4100 a.u.
> In addition, I assign 1.8 for W's radius. If I calculate some molecule
> conataining
> smaller atom, e.g. Cr or Mo, can I use the same radius of 1.8?
> If I use the chelpg charge from gaussian to run MD simulation, can I get
> similar
> results to resp charge?
> Any suggestion or comment are very welcome. I really appreciate it.
> yours
> bob
> ================= supplementary info of
> JOURNAL OF PHYSICAL CHEMISTRY B 112(16): 5153–5162. *DOI*.
> 10.1021/jp710215u
> =====================================
> All Kohn–Sham density functional calculations for polyoxometalates (POM)
> and dendrimer
> ions were performed with the Gaussian03 program package,1 using the
> gradient-corrected
> B3LYP hybrid density functional2,3 (with the VWN-III, not the VWN-V
> functional). Effective
> core potentials (ECP) and associated spherical Gauss-type basis sets of
> Stevens and
> coworkers4,5 were used for all centres (no ECP, only basis set, for
> hydrogen). For the polyoxometalates,
> polarization and diffuse functions (see Table 1 for their exponents) were
> added,
> this basis set is termed SBKJC+(d, f). The basis sets for the dendrimers
> were augmented by
> polarization functions (taken from the Gausssian basis set database) on
> all non-hydrogen
> centres, this basis is termed SBKJC(d). Incremental buildup of the Fock
> matrix was observed
> to cause convergence problems for the POMs, and therefore was disabled.
> For the structure
> optimizations we used an integration grid of 99 radial shells with 590
> angular points per
> shell for all atoms (pruned for nonmetals, unpruned for metals). The
> threshold for maximum
> force was 4.5 · 10−4 a.u., the threshold for maximum displacement in
> internal coordinates was
> 1.8 · 10−3 a.u. This lead to equilibrium structures with energies
> consistent to 10−7 a.u. (the
> same accuracy as for the electronic energy).
> State-averaged MCSCF calculations (using the SBKJC+(d, f) basis set) for
> the states
> 5d46s2 5D, 5d56s1 7S, and 5d6 5D of the tungsten atom were performed with
> the Gamess
> program.6 From the electron densities of these states, radii of density
> isovalue surfaces with
> ½ = 0.002 a.u. were obtained. The arithmetic mean of these radii was taken
> as the Lennard-
> Jones parameter ¾ii for the tungsten atoms.
>
>
>
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Received on Thu Oct 15 2015 - 09:30:03 PDT
