Hi,
I have a peptide fragment with a Cu^2+/Ag^+ accompanying ion. I want to optimise their geometry before I derive partial charges. I thought I would try a couple of different approaches. The first would be:
wb97xd/LANL2DZ - over all atoms. So far, this seems to be consistently converging the SCF.
But with my second effort I decide to use a mixed approach:
wb97xd/GEN
............
C O N 0
6-31+G(d,p)
****
Cu 0
LANL2DZ
This is my first time mixing basis sets, and this is executing so I think I have the syntax alone is correct. However, my issue is with the huge amount of warnings I am getting in the log file. Any insight as to whether this type of calculation is meaningful? Thanks in advance, warning are below......
Pseudopotential Parameters
======================================================================================================
Center Atomic Valence Angular Power
Number Number Electrons Momentum of R Exponent Coefficient SO-Coeffient
======================================================================================================
1 6
No pseudopotential on this center.
2 6
No pseudopotential on this center.
3 6
No pseudopotential on this center.
4 6
No pseudopotential on this center.
5 1
No pseudopotential on this center.
....
....
61 1
No pseudopotential on this center.
62 29 19
D and up
1 511.9951763 -10.00000000 0.00000000
2 93.2801074 -72.55482820 0.00000000
2 23.2206669 -12.74502310 0.00000000
S - D
0 173.1180854 3.00000000 0.00000000
1 185.2419886 23.83518250 0.00000000
2 73.1517847 473.89304880 0.00000000
2 14.6884157 157.63458230 0.00000000
P - D
0 100.7191369 5.00000000 0.00000000
1 130.8345665 6.49909360 0.00000000
2 53.8683720 351.46053950 0.00000000
2 14.0989469 85.50160360 0.00000000
======================================================================================================
Warning: center 5 has no basis functions!
Warning: center 6 has no basis functions!
Warning: center 8 has no basis functions!
Warning: center 9 has no basis functions!
Warning: center 11 has no basis functions!
.......
Warning! H atom 5 has 1 valence electrons but only 0 basis functions.
This is less than a minimal basis set!
Warning! H atom 6 has 1 valence electrons but only 0 basis functions.
This is less than a minimal basis set!
Warning! H atom 8 has 1 valence electrons but only 0 basis functions.
This is less than a minimal basis set!
Warning! H atom 9 has 1 valence electrons but only 0 basis functions.
This is less than a minimal basis set!
.......
Warning! H atom 61 has 1 valence electrons but only 0 basis functions.
This is less than a minimal basis set!
Warning! Cu atom 62 has 19 valence electrons but only 0 basis functions.
This is less than a minimal basis set!
I've tried the following:
C O N 0
6-31+G(d,p)
****
Cu 0
LANL2DZ
****
Cu 0
LANL2DZ
With a blank line between the two Copper atom specifications, the end of file, and after the coordinates. After reading more about pseudo=read and GEN, I understand what is going on, however, Gaussian is still throwing up the same warnings. Is this usual, or have I missed something? I don't mind if I am wrong, I will just keep digging.
Thanks once again.
Here is a similar discussion on research gate: https://www.researchgate.net/post/How_to_use_split_Basis_Sets_for_different_atoms/1
Yesterday I had also this issue. I didn't put any space between them and I started in my case with iodine - this was the only atom. And it worked for me.
I
dgdzvp
**************
C H O
6-311+G**
***************
and here is my output:
General basis read from cards: (5D, 7F)
Centers: 1 22
dgdzvp
**************
Centers: 2 3 5 6 8 10 14 15 16 17 23 24 26 27 29 31 35 36 37 38
Centers: 11 12 13 18 19 20 21 32 33 34 39 40 41 42 4 7 9 25 28 30
6-31G*
***************
Good luck
Hi, Thanks for the suggestion. I've just tried your suggestion and it is still throwing up the exact same warning. I used:
# opt=calcfc wb97xd/gen
.......COORDS HERE...ETC...
H 3.90458800 0.34215900 -2.42184700
N 1.53258000 -2.05749900 0.07764200
H 1.48732400 -2.68568700 0.86697600
Cu -4.22300876 0.96453148 1.16573486
Cu 0
LANL2DZ
****
C O N 0
6-31+G(d,p)
****
I understand this is also different from the first suggestion, and many other suggestions across numerous threads but I'm always getting the same warnings.
Hallo, Anthony!
You have not defined basis sets for H atoms (as in the case of Cu as well)..
As you have a pseudopotential on Cu only, the messages on missing pseudopotentials on remaining centers are for your information only.
Best wishes
mb
As suggest Karsten, if you use a pseudo you need to tell gaussian to read the ecp part.
I use GEN and PSEUDO=READ
Maxime Mercy is right. LANL2DZ basis set uses a pseudopotential for core electrons. Therefore, the keyword pseudo=read has to be used. Then, specify basis sets as written by Travis Pollard but without the stars in the pseudopotential section, i.e. something like
# opt=calcfc wb97xd gen pseudo=read
blank line
title
blank line
charge multiplicity
coords
blank line
Cu 0
LANL2DZ
****
C O N 0
6-31+G(d,p)
****
blank line
Cu 0
LANL2
blank line
blank line
instead of providing the name of the element it is also possible to supply the number of the atom in the list of coordinates. For instance treat atoms 1 and 3 with basisset1 and atom 2 with basisset2
1 3 0
Basisset1
****
2 0
Basisset2
****
this can be interesting if you want to use different basis sets for the same element in a molecular system.
hi
to use psudo potentials you should use in route section for example #T B3LYP/Gen pseudo=read Opt ...etc.......... After insert the coordinates of the molécule specify for each atom the basis function applied
for example,
****
C 0
6-311+G(d).
****
Cu 0
LANL2DZ
****
blank line.
****
Cu 0.
LANL2DZ
off course, in the outcome of gaussian program it will see
no pseudopotential on this center this is normal but it should not any warnings in the calculations
also to get better results use a polarized psudo potentials like
LAN2TZ+ for Cu or Ag cations
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