From owner-chemistry@ccl.net Thu Jul 14 12:05:01 2016 From: "Indrajit Deb biky2004indra---gmail.com" To: CCL Subject: CCL: Problem with Gaussian09 with B97D/def2TZVPPD basis set from EMSL Message-Id: <-52301-160714115302-1630-kG5VhhWi3X2YezC8xLlChw{}server.ccl.net> X-Original-From: "Indrajit Deb" Date: Thu, 14 Jul 2016 11:53:01 -0400 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 From owner-chemistry@ccl.net Thu Jul 14 12:40:01 2016 From: "Pezhman Zarabadi Poor pzarabadip##gmail.com" To: CCL Subject: CCL: Problem with Gaussian09 with B97D/def2TZVPPD basis set from EMSL Message-Id: <-52302-160714123643-22908-CBkNORwbNEZPKkH/qNA9DA===server.ccl.net> X-Original-From: Pezhman Zarabadi Poor Content-Type: multipart/alternative; boundary=001a113df52008d5bf05379b1b80 Date: Thu, 14 Jul 2016 11:36:36 -0500 MIME-Version: 1.0 Sent to CCL by: Pezhman Zarabadi Poor [pzarabadip++gmail.com] --001a113df52008d5bf05379b1b80 Content-Type: text/plain; charset=UTF-8 Dear Indrajit Deb, It's better to send your input file as an attachment. I believe there should be a problem in your input file. It is meaningless that it works for optimization job but does not work for single point calculation. Best wishes, Dr. Pezhman Zarabadi-Poor DGAPA Postdoctoral Fellow Institute of Chemistry National Autonomous University of Mexico (UNAM) Google Scholar Profile On Thu, Jul 14, 2016 at 10:53 AM, 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> > > -- Dr. Pezhman Zarabadi-Poor DGAPA Postdoctoral Fellow Institute of Chemistry National Autonomous University of Mexico (UNAM) Google Scholar Profile --001a113df52008d5bf05379b1b80 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
Dear=C2=A0Indrajit Deb,

It's better to send your input file as an attach= ment. I believe there should be a problem in your input file. It is meaning= less that it works for optimization job but does not work for single point = calculation.

<= /div>
Best wishes,
Dr. Pezhman Zarabadi-Poor

DGAPA Postdoctoral Fellow

Institute of Chemistry

National Autonomous University of Mexico (UNAM)

Google Scholar Profile

On Thu, Jul 14, 2016 at 10:53 AM, I= ndrajit Deb biky2004indra---gm= ail.com <owner-chemistry-$-ccl.net> wrote:

Sent to CCL by: "Indrajit=C2=A0 Deb" [biky2004indra_-_gmai= l.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 error= s
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=3D 0.10000D-02 Tol=3D 0.10000D-05 Strict=3DF.
AO basis set in the form of general basis input (Overlap normalization): ****

Bad length for file.
FileIO: IOper=3D 1 IFilNo(1)=3D -582 Len=3D 0 IPos=3D 0 Q=3D 47472055144592=


dumping /fiocom/, unit =3D 1 NFiles =3D 25 SizExt =3D 524288 WInBlk =3D 512=
defal =3D T LstWrd =3D 596480 FType=3D2 FMxFil=3D10000

...........................................................................=
....................

...........................................................................=
....................

...........................................................................=
....................

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=3D4". Then I found the same error as mentioned abov= e. But for
this supramolecule Optmization calculation is running without any error.
It seems that=C2=A0 B97D/def2TZVPPD basis set with diffusion function (D) i= s 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 calculatio= n
because literature says that for pi-pi interaction it is important. There i= s
a very recent publication few months before where they used B97D/def2TZVPP<= br> 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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--

Dr. Pezhman Zarabadi-Poor

DGAPA Postdoctoral Fellow

Institute of Chemistry

National Autonomous University of Mexico (UNAM)

Google Scholar Profile

--001a113df52008d5bf05379b1b80-- From owner-chemistry@ccl.net Thu Jul 14 14:26:01 2016 From: "Tandon Swetanshu tandons|tcd.ie" To: CCL Subject: CCL: Problem with Gaussian09 with B97D/def2TZVPPD basis set from EMSL Message-Id: <-52303-160714142337-7974-R6ZlmkVJ/ufpfsUiu+Xppg(-)server.ccl.net> X-Original-From: Tandon Swetanshu Content-Type: multipart/alternative; boundary=001a113d027c4b766c05379c995e Date: Thu, 14 Jul 2016 19:23:29 +0100 MIME-Version: 1.0 Sent to CCL by: Tandon Swetanshu [tandons]=[tcd.ie] --001a113d027c4b766c05379c995e Content-Type: text/plain; charset=UTF-8 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> > > --001a113d027c4b766c05379c995e Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
Hi Indrajit,
I think you need to copy the whole basis set from EMSL website def2= TZVPPD for each atom and stick it in your input file. So, in the end your i= nput file will look something like:

#P B97D/Gen SP NoSymm
<= br>
***system definition (coordinates of atoms)***

C 0
copy the basis set for carbon as given on the website
****
H 0=C2=A0
copy the basis set for hydrogen as given on the website****
Similariliy define the basis set for each atom.
The calc= ulation should work then.

Hope that helps,
Sweta= nshu.

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

Sent to CCL by: "Indrajit=C2=A0 Deb" [biky2004indra_-_gmai= l.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 error= s
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=3D 0.10000D-02 Tol=3D 0.10000D-05 Strict=3DF.
AO basis set in the form of general basis input (Overlap normalization): ****

Bad length for file.
FileIO: IOper=3D 1 IFilNo(1)=3D -582 Len=3D 0 IPos=3D 0 Q=3D 47472055144592=


dumping /fiocom/, unit =3D 1 NFiles =3D 25 SizExt =3D 524288 WInBlk =3D 512=
defal =3D T LstWrd =3D 596480 FType=3D2 FMxFil=3D10000

...........................................................................=
....................

...........................................................................=
....................

...........................................................................=
....................

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=3D4". Then I found the same error as mentioned abov= e. But for
this supramolecule Optmization calculation is running without any error.
It seems that=C2=A0 B97D/def2TZVPPD basis set with diffusion function (D) i= s 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 calculatio= n
because literature says that for pi-pi interaction it is important. There i= s
a very recent publication few months before where they used B97D/def2TZVPP<= br> 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



-=3D This is automatically added to each message by the mailing script =3D-=
E-mail to subscribers: CHEMISTRY],[ccl.n= et or use:
=C2=A0 =C2=A0 =C2=A0 http://www.ccl.net/cgi-bin/ccl/s= end_ccl_message

E-mail to administrators: CHEM= ISTRY-REQUEST],[ccl.net or use
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=C2=A0 =C2=A0 =C2=A0 http://www.ccl.net/chemistry/sub_un= sub.shtml

Before posting, check wait time at: http://www.ccl.net

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Conferences: http://server.ccl.net/chemist= ry/announcements/conferences/

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--001a113d027c4b766c05379c995e--