I am frequently asked how to include an extra set of basis functions in a calculation or how to use an entirely external basis set. Sometimes this question also implies the explicit declaration of an external pseudopotential or Effective Core Potential (ECP).
New basis sets and ECPs are published continuously in specialized journals all the time. The same happens with functionals for DFT calculations. The format in which they are published is free and usually only a list of coefficients and exponents are shown and one has to figure out how to introduce it in ones calculation. The EMSL Basis Set Exchange site helps you get it right! It has a clickable periodic table and a list of many (not all) different basis sets at the left side. Below the periodic table there is a menu from which one can select which program we want our basis set for; finally we click on “get basis set” and a pop-up window shows the result in the selected format along with the corresponding references for citation. A multiple query can be performed by selecting more than one element on the table, which generates a list that almost sure can be used as input without further manipulations. Dr. David Feller is to be thanked for leading the creation of this repository. More on the history and mission of the EMSL can be found on their About page. Because of my experience, the rest of the post addresses the inclusion of external basis sets in Gaussian, other programs such as NwChem will be addressed in a different post soon.
The correct format for inclusion of an external basis set is exemplified below with the inclusion of the 3-21G basis set for Carbon as obtained from the EMSL Basis Set Exchange site (blank lines are marked explicitly just to emphasize their location:
spin multiplicity
Molecular coordinates
- blank line -
C 0
S 3 1.00
172.2560000 0.0617669
25.9109000 0.3587940
5.5333500 0.7007130
SP 2 1.00
3.6649800 -0.3958970 0.2364600
0.7705450 1.2158400 0.8606190
SP 1 1.00
0.1958570 1.0000000 1.0000000
****
- blank line -
The use of four stars ‘****’ is mandatory to indicate the end of the basis set specification for any given atom. If a basis set is to be declared for a second atom, it should be included after the **** line without any blank line in between.
WARNING! Sometimes we can find more than one basis set in a single file this is due to different representations, spherical or cartesian basis sets. Gaussian by default uses cartesian (5D,7F) functions. Pure gaussian use 6 functions for d-type orbitals and 10 for f-type orbitals (6D, 10F). Calculations must be consistent throughout, hence all basis functions should be either cartesian or pure.
Inclusion of a pseudopotential allows for more computational resources to be used for calculation of the electronic structure of the valence shell by replacing the inner electrons for a set of functions which simulate the presence of these and their effect (such as shielding) on the valence electrons. There are full core pseudopotentialas, which replace the entire core (kernel). There are also medium core pseudopotentials which only replace the previous kernel to the full one, allowing for the outermost core electrons to be explicitly calculated. The correct inclusion of a pseudopotential is shown below exemplified by the LANL2DZ ECP by Hay and Wadt for the Chlorine atom.
spin multiplicity Molecular coordinates - blank line - basis set for atom1 **** basis set for atom2 (if there is any) **** - blank line - CL 0 CL-ECP 2 10 d potential 5 1 94.8130000 -10.0000000 2 165.6440000 66.2729170 2 30.8317000 -28.9685950 2 10.5841000 -12.8663370 2 3.7704000 -1.7102170 s-d potential 5 0 128.8391000 3.0000000 1 120.3786000 12.8528510 2 63.5622000 275.6723980 2 18.0695000 115.6777120 2 3.8142000 35.0606090 p-d potential 6 0 216.5263000 5.0000000 1 46.5723000 7.4794860 2 147.4685000 613.0320000 2 48.9869000 280.8006850 2 13.2096000 107.8788240 2 3.1831000 15.3439560
If a second ECP is to be introduced, it should be placed right after the first one without any blank line! If a blank line is detected then the program will assume it’s done reading all ECPs and Basis Sets.
Finally, here is an example of a combination of both keywords. If a second ECP was needed then we’d place it at the end of the first one without a blank line. The molecule is any given chlorinated hydrocarbon (H, C and Cl atoms exclusively)
#P B3LYP/gen pseudo=read ADDITIONAL-KEYWORDS
- blank line -
0 1
Molecular Coordinates
- blank line -
H 0
S 3 1.00
19.2384000 0.0328280
2.8987000 0.2312040
0.6535000 0.8172260
S 1 1.00
0.1776000 1.0000000
****
C 0
S 7 1.00
4233.0000000 0.0012200
634.9000000 0.0093420
146.1000000 0.0454520
42.5000000 0.1546570
14.1900000 0.3588660
5.1480000 0.4386320
1.9670000 0.1459180
S 2 1.00
5.1480000 -0.1683670
0.4962000 1.0600910
S 1 1.00
0.1533000 1.0000000
P 4 1.00
18.1600000 0.0185390
3.9860000 0.1154360
1.1430000 0.3861880
0.3594000 0.6401140
P 1 1.00
0.1146000 1.0000000
****
Cl 0
S 2 1.00
2.2310000 -0.4900589
0.4720000 1.2542684
S 1 1.00
0.1631000 1.0000000
P 2 1.00
6.2960000 -0.0635641
0.6333000 1.0141355
P 1 1.00
0.1819000 1.0000000
****
- blank line -
CL 0
CL-ECP 2 10
d potential
5
1 94.8130000 -10.0000000
2 165.6440000 66.2729170
2 30.8317000 -28.9685950
2 10.5841000 -12.8663370
2 3.7704000 -1.7102170
s-d potential
5
0 128.8391000 3.0000000
1 120.3786000 12.8528510
2 63.5622000 275.6723980
2 18.0695000 115.6777120
2 3.8142000 35.0606090
p-d potential
6
0 216.5263000 5.0000000
1 46.5723000 7.4794860
2 147.4685000 613.0320000
2 48.9869000 280.8006850
2 13.2096000 107.8788240
2 3.1831000 15.3439560
- blank line -
If you like this post or found it useful please leave a comment, share it or just give it a like. It is as much fun to find out people is reading as it is finding the answer to ones questions in someone else’s blog 🙂
Peace out!
Dr. Joaquin Barroso's Blog 
Hello dear Dr. Barroso,
Thanks you for your blog, It has helped me several times.
May I have a question about G09.
I would like to do a relaxed PES scan (on dihedral angle) at HF level and a single point at B3LYP level on every step.
I have tried this route:
# B3LYP/6-31G(d)//HF/6-31G(d) geom=modredundant
But the single point is done only on the last step.
I have also tried to do a PES scan and a second calculation with geom=check, again, the single point was done only on the last step.
Could you help me?
Thanks
Thank you very much for your thoughts about the blog!
About your question. I don’t think its possible to do what you are asking to do; not automatically anyway. You would have to do it manually by performing the scan at the HF level and then extracting (with gaussview for instance) the intermediate geometries and do the single point at those geometries.
I must say the methodology sounds very odd. May I ask what is it you are trying to achieve? Is there any reason why you wont do both scans? If you are thinking about “correcting” the energy at each point with the use of DFT let me tell you this is wrong. The energy and geometries achieved belong to different potential energy hyper-surfaces, i.e., results from one, are not necessarily valid on the other.
If you could give me more information I could help you better.
In the mean time I hope this helps.
Best wishes!
Dear Sir,
Your blog is simply superb. Love the way and you write the things.
Your post on Gen ECP using EMSl made my task so easy. Waiting for more posts.
Thanking you,
Nijam,
From India.
Thank you for your kind words Nijamudheen! Keep coming back!
also you can add the basis set, using a file at the end of the geom specification adding the line with @
ie:
%chk=blablabla…
…
…
[coordinates, geom specification, etc]
@./custombasis.gbs (<— file "custombasis.gbs" in the same directory of the gaussian input.).
And so, the extra file content, is printed enterly at the begin of the output log. Sometimes its more easy copy a file and add a line, that recycle a input, modifying molecules hehehe
Mario.
Hi,
Thank you very much for this wonderful blog.
Suppose we wish to use SNSD basis set instead of 6-311++G(d,p) what would be the
corresponding command in the route section?
# opt freq=raman b3lyp/6-311++g(d,p) geom=connectivity
We add @./custombasis.gbs command at the last as suggested at the last
If this basis set is not defined within Gaussian then you have to add it by hand and for that you need the explicit form of it. If you have it then search in this same blog for the usage of an external basis set, we have a blog post on it and it uses the GEN keyword, as in B3LYP/GEN but then you have to list all the values of the basis set at the bottom of the file.
I don’t know why, but I’ve never been able to make the custombasis keyword work, it is just easier for me to paste the entire basis set by hand
I hope this helps and thanks for calling this blog wonderful
Hi Joaquin,
I have been a silent reader of your blog for quite few years and thanks for the excellent job that you do here…!!
Now, I have a question about ONIOM in G09. A TS search I was doing is crashing with an error that I am not familiar with.
Here is the input.
%nprocshared=8
Will use up to 8 processors via shared memory.
%mem=8000MW
%name.chk
# opt=(calcfc,qst3,quadmac,noeigentest,maxcycle=8000) freq=noraman oniom(b3lyp/genecp:uff) nosymm guess=save scf=(qc,maxcyc=7400) geom=connectivity
================================================================
I have a Cd atom in the system, so I am supplying external basis set (LANL2DZ-ECP).
and rest of the atoms are treated with B3LYP/6-31+G(d):uff
now here is the end of the output.
=================================================================
Convergence on expansion vectors, NOT on wavefunctions!
H-V products: 292
Lowest eigenvalue= -0.00688
Eigenvector required to have negative eigenvalue:
QM components of vector:
A5 R6 D18 D17 D104
1 0.43598 -0.37685 -0.36031 -0.31978 -0.29053
D16 R7 D10 A55 D106
1 -0.21855 -0.21495 -0.16994 -0.14925 -0.13923
Largest MM components of vector:
Atom 353 cartesian Z -0.03045
Atom 352 cartesian Z -0.01502
Atom 401 cartesian Z -0.01458
Atom 403 cartesian Z 0.01411
Atom 400 cartesian Z -0.01197
Atom 416 cartesian Z -0.01166
Atom 406 cartesian Z -0.01100
Atom 401 cartesian Y -0.01065
Atom 353 cartesian Y 0.01007
Atom 405 cartesian Y -0.00997
H-V products w/o non-bonded: 30
SchOr2 failed for MMProj.
Error termination via Lnk1e in /opt/scyld/g09/l103.exe at Sun Mar 17 03:41:05 2013.
Job cpu time: 1 days 12 hours 56 minutes 56.7 seconds.
File lengths (MBytes): RWF= 1412 Int= 0 D2E= 0 Chk= 35 Scr= 1
================================================================
All the atoms specified in the output are MM layer hydrogens. I looked at the geometry and couldn’t find anything peculiar with their geometry/connectivity.
Would you please help me to figure out what might be the issue here?
Thanks a lot.
Roby
Thanks a lot.
Thank you very much for a very good blog. The manual is good for understanding the principles for each keyword, but I often find it hard to understand wher to put it inthe inputfile (as in this case), Thank you very much. I have one extra question regardgin this situation though. If I want to use the basis set cc-pvdz for most atoms, but add a diffuse function on only a few atoms (i.e. some H atoms with and some without aug), is the following correct?
title
0 1
atom coordinates
H C N F 0
cc-pvdz
****
8 9 10 2 0
aug-cc-pvdz
****
with thisI intend that all H C N F are described by cc-pvdz except atoms no 8,9,10,2 in the list of atoms
Thank you very much for a useful blog!
Thank you very much for your kind words, Francesca! I’m glad to know this little blog has been helpful to you.
About your question, I must say I’ve never tried something like that but it sounds correct. If it doesn’t work then try doing an explicit listing like:
H 1-10,12-24
cc-pvdz
****
H 11
aug-cc-pvdz
****
…
This sets the first basis set to all H atoms but number 11 which is assigned the augmented basis set in the following line. As I said before I’ve never tried anything of this sort so I can’t say it will work but try both schemes and please let me know if any of them worked.
Have a nice day!
What’s up, after reading this remarkable piece
of writing i am as well happy to share my familiarity here with colleagues.
thank you for your help
Thank you for posting some helpful examples, they really helped me get my custom basis sets calculations up and running quickly.
A quick nit-picky comment about the following however…
“Gaussian by default uses cartesian (5D,7F) functions. Pure gaussian use 6 functions for d-type orbitals and 10 for f-type orbitals (6D, 10F). Calculations must be consistent throughout, hence all basis functions should be either cartesian or pure.”
Pure (spherical harmonic) basis functions use 5 functions at the d-level and 7 functions at the f-level, whereas Cartesian representations require 6 and 10 functions respectively. More generally, for a given angular momentum, L, there are (L+1)(L+2)/2 Cartesian functions and 2*L+1 spherical harmonics, where s -> L=0, p -> L=1, d -> L=2, etc.
All of the actually useful information in your statement is correct however, ie the Gaussian 09 default values and the need for consistency in the representation.
Again thank you for the helpful post.
cheers,
-frank
Hi Dr Barraso,
Thank you for your useful blog. I want to ask you a question. I’m trying to do b3lyp/def2-tzvp calculations for first row transition metal complexes in Gaussian 03. But I had problems while using that GEN keyword. For example my input file is like that:
– – – – – –
chk=name.chk
%NProcShared=8
%mem=10GB
#P opt B3LYP/GEN
Multiplicity
Cordinates
and the basis set from emsl website
– – – – – –
after 129 cycles, there was an error “annihilation of the first spin contaminant, convergence failure…”
so I did same calculation with the output coordinates of that calculation. This time, it said “SCF is confused”, then I added scf=qc keyword to my new calculation, again there was an error “The polynomial fit failed, no lower point found”.
Do you suggest me anything about that? And if i need to use pseudopotentials how can I find those pseudopotentials that fit to my complexes.
Thanks a lot.
Dr. Barroso, Muchisimas gracias por este trabajo. No se imagina la ayuda tan grande que ha sido para nosotros su Blog.
Hello I am so glad I found your weblog, I really found you by mistake, while I was searching on Aol
for something else, Nonetheless I am here now and would just like to say kudos for
a incredible post and a all round exciting blog (I also love the
theme/design), I don’t have time to read it all at the moment but I
have book-marked it and also added your RSS feeds, so when I have time I will be back to read a great
deal more, Please do keep up the awesome work.
excellent issues altogether, you just won a brand new reader.
What may you recommend in regards to your submit that you made some days
in the past? Any positive?
how to optimize a big molecule using oniom method
Dr. Barroso, thank you so much for posting a usefull example, It really helped me to get good results and running quickly. I happy because I now know how can I use gen keyword and pseudo=read in route section.
I’m very glad you found it helpful, Safiya.
Have a nice day
Dr. Barroso, This was useful for me when I used Effective Core pseudopotential, but now I have system of Mg, O, and H and want to use 6-311G* basis set for O and H atoms, and 6-31G for Mg. I try to use Gen keyword without pseudo=read, but gaussian03 did not run. also I added GFprint and GFInput but coefficients of those basis set above which printed in output were not same as of one which are I got from EMSL web site.
pleace, is there another keywords can I use it?
Thanks in advance
Dear Joaquin,
Thank you very much for this really helpful post.
Eider
I’m glad to know its been helpful. Have a nice day and thanks for reading me
Dear Dr Joaquin Barroso,
I’m Dr BAMBA Kafoumba from a University in Côte d’Ivoire.
I’m very interested in your work and I have been following you since I discovered your blog. therefore I thank you so much for brilliant contribution in performing example regarding the use of pseudo-potential through separate basis set.
I’m working now on ruthenium complexes and I have always encountered difficulties to optimize my complexes by that method however I used all keywords necessary for it. Here is my input file and the error I get whenever I perform the calculation.
one of the complexes is RuCl2(Mazpy)2, the calculation was undertaken on both LANL2DZ for Ru atom and 6-31G(d) for the others atoms with the functional B3LYP.
INPUT:
%chk=RUMAZPY_CISCIS_C2_Pseudo_lanl2dz_optfreq_new.chk
%mem=200MW
%nproc=1
# opt b3lyp geom=connectivity gen pseudo=read scf=novaracc
RuCl2Mazpy2_Cis_C2_Pseudo_Lanl2dz_opt
0 1
C -1.97440174 1.28723980 -3.82151621
C -1.93072027 0.11990262 -4.60587127
C -1.75692974 -1.13318443 -3.99416222
C -1.59015323 -1.24628507 -2.59267711
C -1.56918839 -0.04731742 -1.82983206
C -1.80968285 1.22708696 -2.41927810
H -2.15461319 2.26146712 -4.29490424
H -2.05910847 0.18584239 -5.69469038
H -1.76300273 -2.04735405 -4.60250927
C 2.81787575 0.23268614 1.51768020
C 4.05210124 0.34818681 2.24370026
N 1.61451019 -0.12210619 2.16005425
C 4.07152704 0.05471020 3.60237337
H 4.95229250 0.65346289 1.69475922
C 1.68878375 -0.44768015 3.51524536
C 2.87219318 -0.37008127 4.24846341
H 2.86968739 -0.63554889 5.31245448
H -4.95229250 -0.65346289 1.69475922
C -4.05210124 -0.34818681 2.24370026
C -2.81787575 -0.23268614 1.51768020
C -4.07152704 -0.05471020 3.60237337
N -1.61451019 0.12210619 2.16005425
C -2.87219318 0.37008127 4.24846341
C -1.68878375 0.44768015 3.51524536
H -2.86968739 0.63554889 5.31245448
H 1.76300273 2.04735405 -4.60250927
C 1.75692974 1.13318443 -3.99416222
C 1.93072027 -0.11990262 -4.60587127
C 1.59015323 1.24628507 -2.59267711
C 1.97440174 -1.28723980 -3.82151621
H 2.05910847 -0.18584239 -5.69469038
C 1.56918839 0.04731742 -1.82983206
C 1.80968285 -1.22708696 -2.41927810
H 2.15461319 -2.26146712 -4.29490424
N -2.78185136 -0.38497652 0.10768409
N 2.78185136 0.38497652 0.10768409
N 1.44651937 0.11152686 -0.31682494
N -1.44651937 -0.11152686 -0.31682494
Ru 0.00000000 -0.00000000 0.84929315
Cl 0.12642298 2.27661650 1.31594819
Cl -0.12642298 -2.27661650 1.31594819
H -5.00642373 -0.13110304 4.17555941
H 5.00642373 0.13110304 4.17555941
H -0.74739631 0.78724016 3.97138239
H 0.74739631 -0.78724016 3.97138239
C -1.52784104 -2.63980656 -1.94391207
H -1.07753771 -2.60867411 -0.94028599
H -2.55123966 -3.04103804 -1.84337406
H -0.95421461 -3.33195477 -2.57881711
C 1.52784104 2.63980656 -1.94391207
H 1.07753771 2.60867411 -0.94028599
H 2.55123966 3.04103804 -1.84337406
H 0.95421461 3.33195477 -2.57881711
C 1.99842008 -2.49175542 -1.56393403
H 3.01648238 -2.49789319 -1.13676900
H 1.28478299 -2.53998868 -0.72596397
H 1.88368644 -3.39096425 -2.18648109
C -1.99842008 2.49175542 -1.56393403
H -3.01648238 2.49789319 -1.13676900
H -1.28478299 2.53998868 -0.72596397
H -1.88368644 3.39096425 -2.18648109
1 2 1.5 6 1.5 7 1.0
2 3 1.5 8 1.0
3 4 1.5 9 1.0
4 5 1.5 46 1.0
5 6 1.5 38 1.0
6 58 1.0
7
8
9
10 11 1.5 12 1.0 36 1.0
11 13 1.5 14 1.0
12 15 1.0
13 16 1.5 43 1.0
14
15 16 1.5 45 1.0
16 17 1.0
17
18 19 1.0
19 20 1.5 21 1.5
20 22 1.0 35 1.0
21 23 1.5 42 1.0
22 24 1.0
23 24 1.5 25 1.0
24 44 1.0
25
26 27 1.0
27 28 1.5 29 1.5
28 30 1.5 31 1.0
29 32 1.5 50 1.0
30 33 1.5 34 1.0
31
32 33 1.5 37 1.0
33 54 1.0
34
35 38 1.0
36 37 1.0
37 39 1.0
38 39 1.0
39 40 1.0 41 1.0
40
41
42
43
44
45
46 47 1.0 48 1.0 49 1.0
47
48
49
50 51 1.0 52 1.0 53 1.0
51
52
53
54 55 1.0 56 1.0 57 1.0
55
56
57
58 59 1.0 60 1.0 61 1.0
59
60
61
1 2 1.5 6 1.5 7 1.0
2 3 1.5 8 1.0
3 4 1.5 9 1.0
4 5 1.5 46 1.0
5 6 1.5 38 1.0
6 58 1.0
7
8
9
10 11 1.5 12 1.0 36 1.0
11 13 1.5 14 1.0
12 15 1.0
13 16 1.5 43 1.0
14
15 16 1.5 45 1.0
16 17 1.0
17
18 19 1.0
19 20 1.5 21 1.5
20 22 1.0 35 1.0
21 23 1.5 42 1.0
22 24 1.0
23 24 1.5 25 1.0
24 44 1.0
25
26 27 1.0
27 28 1.5 29 1.5
28 30 1.5 31 1.0
29 32 1.5 50 1.0
30 33 1.5 34 1.0
31
32 33 1.5 37 1.0
33 54 1.0
34
35 38 1.0
36 37 1.0
37 39 1.0
38 39 1.0
39 40 1.0 41 1.0
40
41
42
43
44
45
46 47 1.0 48 1.0 49 1.0
47
48
49
50 51 1.0 52 1.0 53 1.0
51
52
53
54 55 1.0 56 1.0 57 1.0
55
56
57
58 59 1.0 60 1.0 61 1.0
59
60
61
C H N Cl 0
6-31G*
****
Ru 0
LANL2DZ
****
RU 0
LANL2DZ
ERROR encountered is:
General basis read from cards: (5D, 7F)
WANTED AN INTEGER AS INPUT.
FOUND A FLOATING POINT NUMBER AS INPUT.
1 2 1.5 6 1.5 7 1.0
?
Error termination via Lnk1e in C:\G03W\l301.exe at Wed May 13 10:18:27 2015.
Job cpu time: 0 days 0 hours 0 minutes 4.0 seconds.
please would help understand what is wrong in my data? and what must I do to come across that issue?
Thank you again
my best regards
Dear Bamba,
Thank you for your nice words about my blog, I’m glad you find it useful.
Please check if you have left a blank line between the coordinates and the connectivity matrix. If you have a blank line, try eliminating the connectivity matrix (1 2 1.0 …) and also the geom=connectivity keyword. That should work.
Have a nice day
Dear joaquinbarroso,
Your blog is really exciting and helpful for the beginners and experienced.I am working with AquaCobalamin and trying to find the TD-DFT for the excited state using TZVP basis set for H and TZVPP for N, Co and O.My professor advised me to do in that way.But unfortunately i cannot getting the result.Everytime it is showing error in log file.Would you please give me some suggestions regrading this.My input file is like this,
%mem=2GB
%chk=T_H2_21d_190.chk
#p TD=(nstates=60) ubp86/genecp nosymm scrf=(solvent=water)geom=connectivity
im co(II) N25 Co18
2 1
C 2.95315160 -2.92421220 -0.68096721
C 1.50726037 -2.46352692 -0.62796122
N 1.42918127 -1.14558893 -0.63790514
C 2.77873183 -0.52441812 -0.79339973
C 3.73090696 -1.63375133 -0.31202809
C 0.35661170 -3.30016994 -0.60450283
C -0.93355969 -2.80889875 -0.61957895
N -1.27997136 -1.46099948 -0.61466906
C -2.63763809 -1.32969640 -0.60928700
C -3.33388878 -2.67199812 -0.66739907
C -2.17186720 -3.68306770 -0.62678892
C -3.32573541 -0.11686874 -0.56340698
C -2.74500475 1.15123476 -0.52938634
N -1.40468868 1.39609038 -0.49823546
C -1.16953020 2.76686772 -0.55369162
C -2.47456580 3.52690436 -0.68449774
C -3.54874413 2.43340413 -0.52685507
Co -0.03952709 0.02270878 -0.47015094
N 1.31950404 1.31373903 -0.35404330
C 1.28692405 2.63348303 -0.39053494
C 2.67973447 3.21609460 -0.23693963
C 3.59479066 1.98304481 -0.46052973
C 2.68791932 0.80617273 -0.05212952
C 0.07326221 3.36621764 -0.51206748
N -0.08322607 -0.08674965 1.42026174
C -0.22732972 0.96260873 2.24836845
N -0.20492731 0.52288222 3.52780486
C -0.03971819 -0.84927593 3.53122660
C 0.03851010 -1.22546746 2.20909086
H 2.93753642 -0.31935714 -1.87251498
H 2.74456059 0.61725118 1.03961238
H -4.41811136 -0.16489962 -0.57243111
H 0.12629039 4.45617871 -0.56605512
H 0.49937897 -4.38345144 -0.59153484
H 0.16852225 -2.21658313 1.78312053
H -0.33866311 2.00441328 1.96093830
H -0.30065938 1.11857798 4.35092091
H 0.00639933 -1.42674562 4.45038944
H 3.86156837 1.89736647 -1.52919026
H 4.52368941 2.02384243 0.12799310
H -4.03459575 -2.78030801 0.17832418
H 2.86219751 4.04290182 -0.94328816
H -2.52268283 4.01311281 -1.67542892
H 2.78629513 3.62966136 0.78480600
H -4.29974214 2.43313366 -1.33433427
H 3.85842553 -1.56855490 0.78359294
H 4.72291410 -1.57632447 -0.78515351
H 3.18998844 -3.27002923 -1.70607253
H 3.13999517 -3.77045254 0.00063289
H -2.54628185 4.32624547 0.07127702
H -2.16061233 -4.36231636 -1.49603764
H -4.10129902 2.52178034 0.42653321
H -2.19468898 -4.31731260 0.27645759
H -3.93469891 -2.74754767 -1.59115760
O -0.11320490 0.17219727 -2.49693354
H 0.23488065 -0.64415352 -2.92279032
H 0.46543962 0.89651228 -2.82863088
1 2 1.0 5 1.0 48 1.0 49 1.0
2 3 2.0 6 1.5
3 4 1.0 18 1.0
4 5 1.0 23 1.0 30 1.0
5 46 1.0 47 1.0
6 7 2.0 34 1.0
7 8 1.0 11 1.0
8 9 1.5 18 1.0
9 10 1.0 12 1.5
10 11 1.0 41 1.0 54 1.0
11 51 1.0 53 1.0
12 13 1.5 32 1.0
13 14 1.5 17 1.0
14 15 1.0 18 1.0
15 16 1.0 24 2.0
16 17 1.0 43 1.0 50 1.0
17 45 1.0 52 1.0
18 19 1.0 55 1.0
19 20 2.0 23 1.0
20 21 1.0 24 1.5
21 22 1.0 42 1.0 44 1.0
22 23 1.0 39 1.0 40 1.0
23 31 1.0
24 33 1.0
25 26 1.5 29 1.0
26 27 1.5 36 1.0
27 28 1.0 37 1.0
28 29 2.0 38 1.0
29 35 1.0
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55 56 1.0 57 1.0
56
57
H 0
TZVP
****
N C O Co 0
TZVPP
****
H 0
TZVP
N C O Co 0
TZVPP
Results are like this,
Rotational constants (GHZ): 0.1985723 0.1958843 0.1393145
Leave Link 202 at Tue Jun 23 16:35:58 2015, MaxMem= 268435456 cpu: 0.1
(Enter /usr/local/g09revc01/g09/l301.exe)
General basis read from cards: (5D, 7F)
Centers: 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49
Centers: 50 51 52 53 54 56 57
TZVP
****
Centers: 3 8 14 19 25 27 1 2 4 5 6 7 9 10 11 12 13 15 16 17
Centers: 20 21 22 23 24 26 28 29 55 18
TZVPP
QPErr — A syntax error was detected in the input line.
TZVPP
‘
Last state=”Top”
TCursr= 933 LCursr= 0
Error reading general basis specification.
Error termination via Lnk1e in /usr/local/g09revc01/g09/l301.exe at Tue Jun 23 16:35:58 2015.
Job cpu time: 0 days 0 hours 0 minutes 3.5 seconds.
File lengths (MBytes): RWF= 80 Int= 0 D2E= 0 Chk= 8 Scr= 8
everytime it says syntax error But when i changes the basis set like as def2TZVP for H and def2TZVPP for N, Co and C the results are like this,
Rotational constants (GHZ): 0.1985788 0.1958872 0.1393147
Leave Link 202 at Thu Jun 25 18:27:22 2015, MaxMem= 268435456 cpu: 0.1
(Enter /usr/local/g09revc01/g09/l301.exe)
General basis read from cards: (5D, 7F)
Centers: 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49
Centers: 50 51 52 53 54 56 57
def2TZVP
****
Centers: 3 8 14 19 25 27 1 2 4 5 6 7 9 10 11 12 13 15 16 17
Centers: 20 21 22 23 24 26 28 29 55 18
def2TZVPP
****
======================================================================================================
Pseudopotential Parameters
======================================================================================================
Center Atomic Valence Angular Power
Number Number Electrons Momentum of R Exponent Coefficient SO-Coeffient
======================================================================================================
WANTED AN INTEGER AS INPUT.
FOUND AN END-OF-LINE FOR INPUT.
def2TZVPP
?
Error termination via Lnk1e in /usr/local/g09revc01/g09/l301.exe at Thu Jun 25 18:27:23 2015.
Job cpu time: 0 days 0 hours 0 minutes 4.7 seconds.
File lengths (MBytes): RWF= 80 Int= 0 D2E= 0 Chk= 8 Scr= 8
Would you please give me any suggestions what to do now?
Thanks,
Mamun
Dear joaquinbarroso,
Your blog is really exciting and helpful platform for beginners . I am working on Amber and I want to optimize reference ligand of my target protein (1M48) before running Molecular Dynamic Simultion. I have prepared reference ligand mol2 file through moe and then convert it into com format without changing coordinates but after resp charge calculation my ligand atom typing is disturbed specially guanidine, amide and carbon carbon triple bond of my ligand. Would you please give me some suggestions regrading this.My input file is like this,
%chk=frg.chk
%mem=2GB
%nproc=2
#P HF/6-31G* SCF=Tight nosymm Geom=Connectivity Pop=MK IOp(6/33=2,6/41=10,6/42=17)
frg_resp
+1 1
N 2.56400000 20.96500000 0.10200000
H 1.74330000 21.53320000 0.25620000
H 3.35510000 21.04090000 0.72530000
C 2.60300000 20.11500000 -0.92400000
N 3.66400000 19.30900000 -1.00600000
H 4.39240000 19.36040000 -0.30820000
H 3.73840000 18.64780000 -1.76580000
N 1.46400000 20.01000000 -1.81600000
C 1.54400000 18.89100000 -2.79600000
H 0.60470000 18.34020000 -2.74730000
H 2.36300000 18.24030000 -2.48960000
C 0.77700000 21.25900000 -2.26300000
H 1.25520000 22.09770000 -1.75700000
H -0.26500000 21.19230000 -1.95030000
C 0.79200000 21.55500000 -3.76800000
H 1.69790000 22.11940000 -3.98900000
H -0.08140000 22.16530000 -3.99770000
C 0.76500000 20.33400000 -4.68500000
H 0.99510000 20.65170000 -5.70200000
H -0.23240000 19.89510000 -4.65840000
C 1.78000000 19.27900000 -4.25600000
H 2.78160000 19.69910000 -4.34800000
C 1.70100000 18.04000000 -5.17200000
H 0.73200000 17.55950000 -5.03720000
H 2.49320000 17.34360000 -4.89710000
C 1.86400000 18.42400000 -6.63000000
O 2.92900000 18.87900000 -7.00900000
N 0.81300000 18.25200000 -7.45500000
H -0.07420000 17.96830000 -7.06450000
C 0.91700000 18.46400000 -8.90300000
H 1.93290000 18.18860000 -9.18610000
C 0.79700000 19.91000000 -9.32700000
O 1.47200000 20.37900000 -10.23500000
O -0.10900000 20.80100000 -8.61900000
C -0.44000000 22.08800000 -9.14000000
H -1.12840000 22.58930000 -8.45960000
H -0.91190000 21.97450000 -10.11600000
H 0.46750000 22.68300000 -9.24230000
C -0.04500000 17.55600000 -9.64200000
H 0.14160000 17.70850000 -10.70500000
H -1.04830000 17.90360000 -9.39570000
C -0.04300000 16.09200000 -9.42200000
C -1.04300000 15.46700000 -8.68000000
H -1.82690000 16.06130000 -8.23420000
C -1.04400000 14.09100000 -8.50700000
H -1.82710000 13.59910000 -7.94920000
C 0.97200000 15.33600000 -9.99400000
H 1.74430000 15.81910000 -10.57420000
C 0.99300000 13.97100000 -9.82100000
H 1.77860000 13.37500000 -10.26160000
C -0.01000000 13.37100000 -9.07200000
C 0.04500000 11.93000000 -8.93200000
C 0.11400000 10.63800000 -8.86200000
C 0.16000000 9.19500000 -8.82400000
C -0.69900000 8.50900000 -9.66900000
H -1.36430000 9.04780000 -10.32740000
C -0.69300000 7.12800000 -9.65800000
H -1.34200000 6.56660000 -10.31380000
C 1.01600000 8.56700000 -7.95600000
H 1.66230000 9.13280000 -7.30130000
C 1.02300000 7.18900000 -7.94800000
H 1.69550000 6.65850000 -7.29030000
C 0.16800000 6.47900000 -8.78300000
H 0.17350000 5.39950000 -8.75050000
Hello, Dr. Joaquin Barroso. Help me with adding an external basis set, please! I Have:
%chk=F:\g09w\UDISEF.chk
# opt b3lyp/Gen pseudo=read
Title Card Required
0 2
Sm 2.23980000 1.03110000 4.37760000
S 2.94980000 -1.49240000 3.30800000
etc.
1 2 1.0 9 1.0 14 1.0 26 1.0 38 1.0 49 1.0 60 1.0 71 1.0
etc.
H 0
S 3 1.00
18.7311370 0.03349460
2.8253937 0.23472695
0.6401217 0.81375733
S 1 1.00
0.1612778 1.0000000
****
Any atom basis
****
Sm 0
уес.
****
SM 0
SM-ECP 5 28
h-ul potential
1
2 1.000000000 0.000000000
s-ul potential
1
2 22.344471000 572.985332000
p-ul potential
1
2 16.694590000 272.359145000
d-ul potential
1
2 13.727705000 115.293900000
f-ul potential
1
2 24.059092000 -51.108392000
g-ul potential
1
2 20.197249000 -25.421885000
But, in .out-file i have error:
Rotational constants (GHZ): 0.0645388 0.0277158 0.0268049
General basis read from cards: (5D, 7F)
WANTED AN INTEGER AS INPUT.
FOUND A FLOATING POINT NUMBER AS INPUT.
1 2 1.0 9 1.0 14 1.0 26 1.0 38 1.0 49 1.0 60 1.0 71 1.0
?
Error termination via Lnk1e in F:\g09w\l301.exe at Thu May 05 12:28:43 2016.
Job cpu time: 0 days 0 hours 0 minutes 2.0 seconds.
File lengths (MBytes): RWF= 42 Int= 0 D2E= 0 Chk= 1 Scr= 1
I don’t understand – have I done something wrong?’
Hello dear Dr. Barroso,
THANKS FOR THE INFORMATION THAT YOU POST IN YOUR WEBSITE AND ITS SO NICE AND GENEROUS THAT YOU SHARE YOUR KNOWLEDGE WITH OTHERS.I HAVE BEEN WORKING WITH GUASSIAN FOR 4 YEARS I HAVE DINE SO MANY CALCULATION BUT I HAVE GOT PROBLEM WITH OPTIMIZING BINUCLEAR METAL COMPLEX I CANT OPTIMIZE THEM WHEN I RUN THE JOB TITTLE IT DOESN’T WORK WOULD YOU PLEASE HELP ME AND GIVE ME A ROUTE SECTION FOR OPTIMIZING BINUCLEAR SHCIFF BASE COMPLEX.?
THANKS
IMAN
Thanks for your kind words! I’ve done it before without a problem. I cannot help you if I don’t know what the error is but probably this is due to some memory issue.
Hi,
This has been very helpful for me to understand the formatting of Gaussian input. I am very new to gaussian and have been trying to optimize a structure with little luck. I keep getting the error: WANTED A STRING AS INPUT.
FOUND A FLOATING POINT NUMBER AS INPUT.
Ag 47.0 5.85071611 3.57892108 3.13763404
Would you possibly be able to tell me what is wrong in my input file?
My input file is set up like this:
%chk=name.chk
%nproc=16
%mem=4GB
# B3LYP/genECP opt freq=noraman gfprint pseudo=read
-blank line-
info
-blank line-
1 1
coordinates (complex has Ag, S, N, C, H and charge of +1)
-blank line-
Ag 0
SDD
****
S N C H 0
6-31G*
****
-blank line-
Ag 0
SDD
-blank line-
Thank you so much!
Jenny
Thank you, I’m glad it’s been helpful.
Try changing GenECP for just Gen and then also add the keyword pseudo=read. Leave the rest of your input the same and let me know if it works or not.
I hope this helps!
i add Te atom to the fullerene molcule in gaussian 9 program .but when running the program appear error
how I traet THIS ERROR ?
basis set used 6-31G d,p
functional B3LYP
IN DFT method
The 6-31G** basis set as defined in Gaussian does not include fourth row elements. You have to go to https://bse.pnl.gov/bse/portal and search for available basis set for Te, download it in the gaussian format and then insert it in your input file as described in this post.
If I remember correctly, there is no 6-31G for Te so you should get another kind of double zeta basis set; I’ve worked with Dunning’s triple zeta basis set for Te in organometallic compounds.
I hope this helps
how insert basis set LAN2LD to the gaussian 9 program Te atom to the fullerene molcule
You cannot. This basis set is not defined for a heavy atom. You need to go to https://bse.pnl.gov/bse/portal download a suitable double zeta basis set for Te and insert it in your input file accordingly to the instructions in this post.
I hope this helps!
Dr.barroso
I want to running togehter two basis set in GO9 to Te added to the fullerene molcule
6-31G d,p and NAL2LD to compute electronic properties
help me please
Dear Dr. Barroso, Thanks a lot for this post on using the GEN keyword. I have explicitly failed in the PBC calculation whenever I use the Gen keyword. So I’m going to try what you have explained.
I have another question. When a pbc run is done after setting up the crystal surface which is cleaved along a certain direction etc. etc., I always find that the contents of the cell which I perfectly set to be within the cell to start with has been moved out of the cell (not the entire thing but part of it. So if I’m studying a slab structure, all my specifications of how deep the vacuum layer is with respect to the contents will be different after optimization. I was going to post a screenshot of the input and output structures but can’t figure out a way to do it here.
Do you know why this happens or how to correct it?
Thanks.
Never really had too much experience working with the PBC module in Gaussian, send me the screen shot via a dropbox or google drive link. What is the route section you are using?
If I understand correctly, you want to optimize the slab but I don’t think the contents of the cell extract are constrained by the cell parameters, but I’m not sure. Send me more details to make a better suggestion.
Have a nice day
Dear Dr. Barroso, thank you for your reply. I’m not that used to blogging and that’s why this got delayed. I have copied the google drive links of the files which show the input and output structures of a surface I optimized using PBC in g09. As I mentioned before, the silica surface has moved out of the cell after optimization. I have also copied the input file with the route section. If you happen to know how to correct this issue, please let me know. Thanks a lot.
https://drive.google.com/file/d/0B5gsEw4UdAlYZk5wZzhoODJ6TFk/view?usp=sharing
https://drive.google.com/file/d/0B5gsEw4UdAlYbnlKV3Z4UFlIMVk/view?usp=sharing
dear Dr. Barroso,
when I run gussian 09 with DFT method by B3LYP / 6-31G(d,p) basis set to calculate electronic properties of formyl (CCL2O ) gas adsorbed fullerene (C59Cl). the G 09 no completed because appear this error (severe Error Message =2070
the processing of the last link ended abnormally. All processing has been aborted. the output file will now open. please see the end of the output file for additional information.
Dear Dr. Barroso,
I have to optimize a geometry with def2-TZVPP basis set for all atoms (H C N). For that, I followed one of your blog and made the input file. But the job is terminating with the error,
General basis read from cards: (5D, 7F)
QPErr — A syntax error was detected in the input line.
‘
Last state=”Top”
TCursr= 927 LCursr= 0
Error reading general basis specification.
Can you please help me for this.
Thank you
Dear Neha,
Can you show me your input? Did you generalize the basis set or directly put in the input stream?
Hello Dr. Barroso,
I’m trying to run QST2 and QST3 simulations with a split basis set, but due to the nature of these simulations requiring multiple coordinates (reactant, product, and transition state guess for QST3), I’m having difficulty figuring out where to specify the basis set.
To illustrate, my system has C, H, O, Si, and Cr atoms. I tried the following input file for the QST2 simulation first:
#p wb97xd/gen nosymm opt=(QST2)
Title Card
0 4
0 4
Cr 0
def2TZVP
****
O Si C H 0
TZVP
****
This resulted in an immediate error, indicating the input file had not been set up properly. So I tried it again, as follows:
#p wb97xd/gen nosymm opt=(QST2)
Title Card
0 4
Cr 0
def2TZVP
****
O Si C H 0
TZVP
****
0 4
Cr 0
def2TZVP
****
O Si C H 0
TZVP
****
This modification was still to no avail. Do you have any recommendations for how to set up the input file properly with this split basis set? Any advice would be greatly appreciated.
Pardon me, it was supposed to say [coordinates of reactant] or [coordinates of product] underneath the 0 4 multiplicity lines.
Hello,
Interesting, I’ve never had to combine gen with a transition state search. I’m inclined to think it should be the first option but that you missed the title card for the products, have you checked that?
If you could share the error message section in the output it would be easier to find the problem. Alternatively, if you please, send me your input/output files so I can help you better. jbarroso-at-unam-mx
Ah yes, the title card was in the actual file, so that’s not the problem. I’ll send you the files, thank you!
The first input in which the external basis set is defined at the end of the input file is the correct structure. Your error relates to a problem with finding a suitable path along the potential energy surface to connect -in one go- those two structures. Gaussian needs a lot of chemistry insight when it comes to finding TS, hence we titled the post ‘the art of finding TS’. Pre-optimize reagent and product and use those coordinates in the QST2 input. Also, consider using the QST3 method and give Gaussian a little more help in the right direction.
I hope this helps
Greetings from a PhD student from China. I always enjoy reading your blogs.
Thank you very much, I’m glad to know you like it.
Hello Dr. Barroso,
My problem is
The calcul stops without an error
#p opt=(maxcyc=1000) wb97xd/6-31g(d,p) scrf=(solvent=water) scf=qc geo
m=connectivity
An expanding polynomial of degree 2 produced 0.6034
You probably don’t have enough disk space to make it work.
Hi, Dr. Joaquinbarroso, please help me to deal with this.
I added B3LYP/6-31G(d,p) for another atoms and LANL2DZ for Ti as mentioned in papers, however, the calculation was kept being terminated, I do not know whether any error with my input file.
Please help me to figure out and let me know.
Thank you so much.
%nprocshared=16
%mem=40GB
%chk=TiO2_anatase101_only_LAN.chk
# opt b3lyp/genecp geom=connectivity 5d 7f pseudo=read scrf=(pcm,solvent=generic,read)
Title Card Required
0 1
Ti 1.57066900 1.70134200 1.57985400
O 0.89553800 1.56607600 -0.02689900
O -0.24017900 1.25702300 2.38640400
O 1.28857200 3.63187200 1.81328600
O 2.75176700 0.18625600 1.19910100
Ti -1.66539200 0.03696100 1.65810100
Ti 0.51626500 1.43624100 -1.89299700
Ti -0.34707600 4.63147000 1.80831800
Ti 3.16163900 4.33995900 1.10095100
Ti 3.06637900 -1.51712000 1.76485800
O -2.99106400 1.75055600 1.48858200
O -0.65112600 -1.40844500 1.97877800
O -3.16497100 -0.55362400 2.53151500
O -1.89142300 -0.11346600 -0.12765500
O -0.87776400 0.43966800 -2.66579400
O 1.85796800 1.80992600 -3.10248200
O -0.37085100 2.97003600 -1.92709700
O 1.73573900 -0.35888000 -1.83157200
Ti 1.36883400 7.14646500 1.04950800
Ti -2.85034700 3.48088900 1.18002600
O -1.18362600 4.24345200 0.28313300
O -1.81247100 4.05875900 2.66633200
O -0.15722900 6.46457900 1.82196700
O 3.50269000 2.50989700 1.45780600
O 4.82094400 5.07709400 0.64692000
Ti 4.50895300 5.13548400 -1.12718200
O 2.93648500 4.30113000 -0.67097300
O 2.54802500 6.05800100 1.71709400
Ti 0.46131000 -2.82448100 1.65543200
O 1.78250500 -2.02158900 0.45436300
O 1.83510400 -2.48962900 2.78844700
O 4.11404100 -2.87699200 0.82994800
Ti -4.64759400 0.36764100 2.02877400
Ti -2.31747400 -0.20955600 -1.86599200
Ti 3.28544400 0.70661400 -2.86157300
Ti -1.55914000 4.35479000 -1.82760500
Ti 1.45642400 -2.03564900 -1.42458900
O 2.28663900 8.57127400 0.20285400
Ti 2.45855500 7.84477200 -1.45697300
O 1.22396900 6.53864400 -0.74506900
Ti -6.03547600 3.30825600 1.72975400
O -4.50718500 4.27190300 1.44427000
Ti 4.55071900 1.07774900 0.69595300
O 3.93101200 6.76668300 -1.77304700
O 5.63046600 3.89278200 -1.92028600
O -0.66174100 -4.01473800 2.87185500
Ti 4.70525800 -4.57759700 0.68356200
Ti 6.03137400 -2.02310300 0.41253700
O -5.46313400 1.98937500 2.67983400
O -5.98347800 -0.63550300 2.60904800
O -5.27298700 -0.12526000 0.29534000
O -3.82232200 0.89280000 -2.15527400
O -2.41908300 -2.03268200 -2.25576700
O 3.75495100 -0.90344100 -3.74822000
O 4.66634500 1.72299600 -3.39698600
O 4.04925300 1.07892500 -1.12301600
Ti -0.10281200 6.73779800 -2.22307100
Ti -3.90645400 2.81521000 -2.32835800
O -2.70488200 3.82865200 -3.22488100
O 0.01550200 5.25241400 -3.01451700
O -3.12696700 3.40414100 -0.84396500
O -1.68558400 6.21538200 -1.48698500
Ti -0.97084400 -3.31163200 -1.96207500
O 0.39143300 -2.69871900 -2.89617600
O -0.30227900 -2.63962800 -0.49174500
O 3.01893400 -2.97580900 -1.97280300
O 1.21115100 8.09923300 -2.70928800
O -7.92060700 3.32531600 1.98016500
Ti -8.41537400 2.11772100 0.73461800
O -6.54852700 2.35492500 0.12919800
O 5.19252400 -0.62062400 1.34084600
O 5.96703900 1.95973900 0.13998400
Ti 5.62425400 2.07377800 -1.80433900
Ti -0.70820700 -5.58253900 2.13392700
O 4.44926800 -5.19786800 -1.00299700
O 6.40030100 -3.80747600 0.77359100
O 3.63053500 -5.65831900 1.70890000
O 7.61565400 -1.42893400 -0.28566500
Ti 7.11543500 -0.91863800 -2.00307000
O 5.40701300 -1.55729900 -1.36515700
Ti -6.93365200 -0.99965000 0.98188400
Ti -5.74888500 -0.35090700 -1.58143000
Ti -4.09868000 -3.22702200 -1.80551500
Ti 4.79678700 -2.20055200 -3.11655500
Ti -7.02443200 2.63966900 -1.70395900
O -5.57382700 3.59724700 -2.28785900
O -0.24170600 -5.11016500 -1.55323700
Ti 3.47057100 -4.68340800 -2.46296600
O -8.22282000 0.37348200 1.17763100
O -8.75329800 2.66937400 -0.97885200
O 7.00921300 0.84047700 -2.17524900
Ti 1.90563600 -6.13615400 1.22033300
O 0.85789500 -4.70847500 0.98553900
O -2.22282800 -6.60611200 2.64925900
O 0.74353600 -6.75354200 2.44981500
Ti -3.31033300 -6.38007700 1.21520000
O -1.89253500 -5.38044900 0.51832400
O 6.54310200 -1.75960000 -3.53570000
O -6.74592600 -2.84131500 1.14194600
O -7.18759500 -1.11576900 -0.90561800
O -6.68607600 1.07275000 -2.40742100
O -5.02285000 -1.72794900 -2.47318300
Ti -5.46504700 -3.94526100 0.45416000
O -4.02933200 -2.90909900 -0.03905900
O -5.53650100 -4.31792900 -1.32374600
O -2.70864900 -4.59282300 -2.14913800
O 4.61922900 -3.96427000 -3.67772500
Ti -2.00985700 -6.14746400 -1.31741800
Ti 0.77759800 -6.53724300 -1.91216800
O 2.13592900 -5.81758500 -2.97012200
O 1.60258800 -7.01490300 -0.39257000
O -4.75633900 -5.30699200 1.46011000
O -3.30438400 -7.14531000 -0.47148000
O -0.88967500 -7.41641900 -2.02910400
1 2 1.0 3 1.0 4 1.0 5 1.0 24 1.0
2 7 1.0
3 6 1.0
4 8 1.0
5 10 1.0 43 1.0
6 12 1.0 13 1.0 14 1.0
7 15 1.0 16 1.0 17 1.0
8 21 1.0 22 1.0 23 1.0
9 24 1.0 25 1.0 26 1.0 27 1.0 28 1.0
10 30 1.0 31 1.0 32 1.0
11 20 1.0
12 29 1.0
13 33 1.0
14 34 1.0
15 34 1.0
16 35 1.0
17 36 1.0
18 37 1.0
19 23 1.0 28 1.0 38 1.0 40 1.0
20 21 1.0 22 1.0 42 1.0 61 1.0
21
22
23
24 43 1.0
25 26 1.0
26 27 1.0 44 1.0 45 1.0
27
28
29 30 1.0 31 1.0 46 1.0 93 1.0
30 37 1.0
31
32 47 1.0
33 49 1.0 50 1.0 51 1.0
34 52 1.0 53 1.0
35 54 1.0 55 1.0 56 1.0
36 59 1.0 61 1.0 62 1.0
37 63 1.0 64 1.0 65 1.0 66 1.0
38 39 1.0
39 40 1.0 44 1.0 67 1.0
40 57 1.0
41 42 1.0 49 1.0 68 1.0 70 1.0
42
43 56 1.0 71 1.0 72 1.0
44
45 73 1.0
46 74 1.0
47 75 1.0 76 1.0 77 1.0
48 71 1.0 76 1.0 78 1.0 80 1.0
49
50 81 1.0
51 81 1.0 82 1.0
52 58 1.0
53 63 1.0
54 84 1.0
55 73 1.0
56 73 1.0
57 60 1.0 62 1.0 67 1.0
58 59 1.0 61 1.0 86 1.0
59
60
61
62
63 64 1.0 65 1.0 87 1.0
64
65
66 88 1.0
67
68 69 1.0
69 70 1.0 89 1.0 90 1.0
70 85 1.0
71
72 73 1.0
73 91 1.0
74 94 1.0 95 1.0 97 1.0
75 88 1.0
76
77 92 1.0
78 79 1.0
79 80 1.0 91 1.0 98 1.0
80 84 1.0
81 89 1.0 99 1.0 100 1.0
82 100 1.0 101 1.0 102 1.0
83 102 1.0 103 1.0 104 1.0 105 1.0 106 1.0
84 98 1.0 107 1.0
85 86 1.0 90 1.0 101 1.0
86
87 108 1.0 109 1.0
88 107 1.0 110 1.0
89
90
91
92 93 1.0 95 1.0 111 1.0
93
94 96 1.0
95
96 97 1.0 112 1.0 113 1.0
97 108 1.0
98
99 103 1.0
100
101
102
103 104 1.0 105 1.0 112 1.0
104
105
106 108 1.0
107
108 113 1.0 114 1.0
109 110 1.0 111 1.0 114 1.0
110
111
112
113
114
O 0
6-31G(d,p)
****
Ti 0
LANL2DZ
****
Ti 0
LANL2DZ
Eps=36
EpsInf=1.9684
Hi Hieu
If you could copy the last few lines of your output file with the error I could be able to help. But I think it might have to do not with the ECP portion but the SCRF reading options. Also there seems to be a weird symbol for those atoms which aren’t Ti; not sure if you copied them like that or instead deleted them to protect the identity of your system 🙂
Have a nice day
Hello! Thank you for your blog! I was wondering if you could elaborate on the numbers below the specified basis sets. I included an example below that was shared with me, but I am having difficulty figuring out how to determine the numbers that should follow “D” (in this case 1 and 1.00) and then what the numbers on the following lines mean/where they come from (0.8 and 0.65) for F C N O and then S. Thank you!
Pd 0
CEP-31G
****
F C N O 0
CEP-31G
D 1 1.00
0.8000000 1.0000000
****
S 0
CEP-31G
D 1 1.00
0.6500000 1.0000000
****
H 0
CEP-31G
****
Pd S C N O F 0
CEP-31G
Hello Kiana
So the “D 1 1.00” means one single d function without scaling (or more precisely with a scaling factor of 1.00) is used. If two gaussian functions were to be used for this d orbital then the line would look like “D 2 1.00”
The following line are exponents and coefficients for the construction of this function, each gaussian function has the form c*exp{-zr^2} where c is the coefficient 0.800000 and the exponent is z = 1.000000
You may also some times have something like:
SP 2 1.0
number1,1 number1,2 number1,3
number2,1 number 2,2 number2,3
Where SP means the same exponents are used for S and P functions, hence number1,1 is the exponent and number1,2 and number1,3 are the coefficients for the first (of the 2 in SP 2 1.00) gaussian function used to construct this orbital.
It’s straightforward once you get the hang of it but I’ll admit it took me a while to get it down back in the old days. 🙂
I hope this helps
Hi Joaquín, I’ve got a question:
I want to use the basis set aug-cc-pVT(+d)Z on G16 and upload it to the cluster, but my opt-freq calculation did not work. From this post, I gather that I should put “gen” before the basis set?
Example:
%nprocshared=8
%mem=12GB
%chk=water.chk
# opt(verytight, calcfc) freq b3lyp/gen aug-cc-pVT(+d)Z
Please, correct me if I’m wrong.
Thanks!
Hola Francisca!!
The GEN keyword works to include a basis set that is not defined within gaussian (or to assign different basis sets to different atoms). If this basis set is not defined in Gaussian16 then you need to download it first from a place such as the EMSL basis set exchange in the proper format. Therefore, mixing gen and *any basis set* in the route section might cause a conflict for the program.
I hope this helps!
Hi Joaquin,
This is my input file. I am trying to obtain esp charges. But it is ending up in error. I hope you could help me.
# b3lyp/genecp scrf=(solvent=water) pop=(mk,readradii) geom=connectivity pseudo=read scf=tight
Title card
-1 1
C 7.71877800 -1.95155800 3.17517700
C 6.43365500 -2.49696200 3.09491600
C 8.25426800 -1.28699400 2.06838900
C 5.69328300 -2.38816100 1.91670600
.
.
.
.
.
H 5.48773500 -2.80108600 -2.16718300
H 7.01734400 -2.71494300 -1.31226300
N -6.31030100 -5.16626800 3.11412900
Cd -1.51463600 5.62006900 0.91545000
1 2 1.5 3 1.5 28 1.0
2 4 1.5 41 1.0
3 5 1.5 42 1.0
4 6 1.5 43 1.0
5 6 1.5 44 1.0
6 27 1.0
.
.
.
.
.
.
60
61
62
63
64
65
66
C H O 0
6-31g(d)
****
N 0
6-31g(d)
****
Cd 0
sto-3g
****
blank line
Cd 0.95
blank line
blank line
The error in the output file is
WANTED AN INTEGER AS INPUT.
FOUND A FLOATING POINT NUMBER AS INPUT.
Cd 0.95
?
Error termination via Lnk1e in /opt/software/g09/l301.exe
Thank you
Dear joaquinbarroso,
I am optimizing a molecule to get the parameters from cgenff. For that I am using Gaussian, Here one of step is to optimize the dihedral. But I have no idea which dihedral of the molecule should be optimized and what should be the inputs.
can you help me?
Eagerly waiting for your response.
Thank you
Dear Farinda,
Please take a look at this post (https://joaquinbarroso.com/tag/partial-optimization/) for a partial optimization so you may optimize only the dihedral angle you want. As to what dihedral to optimize, that depends on your molecule and what you want to do with it; I’m afraid I cannot help you with that part with as little information as this.
I hope this helps
How to add additional keyword in the input for optimisation of metal complex