CCL:G: Problem with Gaussian09 with B97D/def2TZVPPD basis set from EMSL

Hi Pezhman and Swetanshu,

Thanks to you both for replying. Finally I solved the problem. And fortunately the problem was with the input file. I am trying to explain. May be it will help others.

1. I was running both Optimization and SP calculation with the same B97D/def2TZVPPD external basis set (downloaded from EMSL).
2. In the Optimization calculation there was two blank lines at the end of the external basis set file (as it was downloaded) and one blank line at end of Gaussian09 input file. It was running successfully.
3. So, I decided to use same strategy of blank lines during the SP calculation. But It was crashing.
4. Solve: I removed all the blank lines from the end of the external basis set file, but kept one blank line at end of Gaussian09 input file (as a general rule). Its running.
5. Another point to be noted----do not keep any blank lines at the beginning of the external basis set file.

But now I have one more problem.

The SP calculation with B97D/def2TZVPPD basis set is not converging. My system has four nucleic acid base rings --all are optimized with the B97D/def2TZVPPD basis set. They are oriented in the space in a specific manner which I can not alter. Because these orientations are from MD simulations. Is there any way to use loose convergence criteria in this DFT calculation. For information, the calculations are converging with B97D/def2TZVPP basis set (without diffuse function). I want to use the diffuse function.

I am very new in this calculations. Any help will be useful.

Thank you,

----indrajit 
    




--------------------------------------------------------------------------------------------------------------
Indrajit Deb
Present Position
International Centre for Genetic Engineering and Biotechnology (ICGEB, Italy) SMART Fellow, 
Department of Structural Chemistry and Biology of Nucleic Acids, 
Institute of Bioorganic Chemistry (IBCh), 
Polish Academy of Sciences (PAS). 
European Center for Bioinformatics and Genomics (ECBiG) Campus (
R
oom: 2.6.28
). 
Z. Noskowskiego Str. 12/14. 
Poznan 61-704, Poland​. 
Phone: +48616653042, ​Personal Mobile: +48662513522​
​
Previous Position​
Ph.D Student, 
Department of Biophysics, Molecular Biology and Bioinformatics, University of Calcutta (CU), 92 APC Road, Kolkata - 700009, India. Phone: +913323508386 (extn. 329, 321), Fax: +913323519755. Personal Mobile: +919239202278 

On Thu, Jul 14, 2016 at 8:23 PM, Tandon Swetanshu tandons|tcd.ie <owner-chemistry%%ccl.net> wrote:
Hi Indrajit,

I think you need to copy the whole basis set from EMSL website def2TZVPPD for each atom and stick it in your input file. So, in the end your input file will look something like:

#P B97D/Gen SP NoSymm

***system definition (coordinates of atoms)***

C 0
copy the basis set for carbon as given on the website
****
H 0 
copy the basis set for hydrogen as given on the website
****
Similariliy define the basis set for each atom.
The calculation should work then.

Hope that helps,
Swetanshu.

On 14 July 2016 at 16:53, Indrajit Deb biky2004indra---gmail.com <owner-chemistry:_:ccl.net> wrote:

Sent to CCL by: "Indrajit  Deb" [biky2004indra_-_gmail.com]
Hi,

I am facing some problems with G09.

My objective is to calculate the interaction energy between RNA bases for
the geometries extracted from MD simulation run in AMBER.

My problem is as follows.....

I am optimizing four individual nucleic acid bases with B97D/def2TZVPPD
basis set. The def2TZVPPD basis set. I have downloaded it from EMSL website.
Because G09 don't have this diffusion function and we have license for only
G09. Anyway G09 have def2TZVPP without the diffuse function (D).

I am using the following input.......

#P B97D/Gen Opt(ModRedundant) NoSymm

------------------------------------------------------------

++./Def2-TZVPPD

There was nothing wrong with the optimization.

But when I tried single point (SP) energy calculation with the same basis
set and same geometry that I used during optimization, there are some errors
and calculation is terminating. The input is as follows..........

#P B97D/Gen SP NoSymm

------------------------------------------------------------

++./Def2-TZVPPD

The errors are as follows........

(Enter /home/indra/g09/g09/l301.exe)
General basis read from cards: (5D, 7F)
Warning: center 1 has no basis functions!
Warning: center 2 has no basis functions!
Warning: center 3 has no basis functions!
Warning: center 4 has no basis functions!
Warning: center 5 has no basis functions!
Warning: center 6 has no basis functions!
Warning: center 7 has no basis functions!
Warning: center 8 has no basis functions!
Warning: center 9 has no basis functions!
Warning: center 10 has no basis functions!
Warning: center 11 has no basis functions!
Warning: center 12 has no basis functions!
Warning: center 13 has no basis functions!
Warning: center 14 has no basis functions!
Warning: center 15 has no basis functions!
Ernie: Thresh= 0.10000D-02 Tol= 0.10000D-05 Strict=F.
AO basis set in the form of general basis input (Overlap normalization):
****

Bad length for file.
FileIO: IOper= 1 IFilNo(1)= -582 Len= 0 IPos= 0 Q= 47472055144592


dumping /fiocom/, unit = 1 NFiles = 25 SizExt = 524288 WInBlk = 512
defal = T LstWrd = 596480 FType=2 FMxFil=10000

...........................................................................
....................

...........................................................................
....................

...........................................................................
....................

Error termination in NtrErr:
NtrErr Called from FileIO.

Further, I took the geometries of the four optimized nucleic acid bases as a
supramolecule and tried to calculate the single point energy with
"Counterpoise=4". Then I found the same error as mentioned above. But for
this supramolecule Optmization calculation is running without any error.

It seems that  B97D/def2TZVPPD basis set with diffusion function (D) is not
working for single point energy (SP) calculation. To verify this I tried
both the optmization and single point energy calculation using
B97D/def2TZVPP basis set (available in G09). Both the calculation completed
successfully.

I want to use B97D/def2TZVPP with the diffuse function (D) in my calculation
because literature says that for pi-pi interaction it is important. There is
a very recent publication few months before where they used B97D/def2TZVPP
basis set without the diffuse function.

It will be really nice if anyone can help. Looking forward to some
responses. I can attach the input files if anyone need.

Thanking you,

Indrajit Deb



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