Hi AMBER users,
I am facing some problems with G09. I know that It is an AMBER mailing
list, but I am sure that there are some experts for quantum calculation
also.
My objective is to calculate the interaction energy between RNA bases for
the geometries extracted from MD simulation run in AMBER.
It seems that this could be a place where I can get my answer. 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
--------------------------------------------------------------------------------------------------------------
*Indrajit Deb*
alternate emails: indrajitdeb81.gmail.com, idbmbg_s.caluniv.ac.in
*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
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Received on Thu Jul 14 2016 - 06:00:02 PDT
