Hi Renato,
you can address that problem by providing the missing vdW radius for
Selenium in your input file.
In the keyword line of your Gaussian input simply replace
Pop=MK
by
Pop=(MK,ReadRadii)
and then add, after your coordinate section and a blank line, the
element name and the atomic radius in Angstroem
(cf: http://gaussian.com/population/?tabid=1#Pop_keyword__ReadRadii_option)
Which radius you want to use here, I cannot tell. For a quick test, I
just used the wikipedia value of 1.20.
However, I'd recommend to separate geometry optimization and ESP
calculation into two jobs, because the optimization does work for Se in
any case.
Keyword line for optimization:
# HF/6-31G* SCF=tight test opt
Then copy the checkpoint file to a new name and read the geometry and
wavefunction information from there in the next step
# HF/6-31G* SCF=tight Test Pop=(MK,ReadRadii) iop(6/33=2) iop(6/42=6)
iop(6/50=1) geom=check guess=read
nulla rosa sine spina
0 1
Se 1.20
Hope that helps.
Regards,
Anselm
NHR.FAU
Friedrich-Alexander-Universität Erlangen-Nürnberg
Germany
On 06/30/2021 11:44 PM, Renato Araujo wrote:
> Dear Amber Users
>
> I'm trying to perform a molecular dynamics simulation of a protein-ligand.
>
> My ligand has a Selenium element in its structure.
>
> In the step of calculating the loads of the ligand using the g09 program I
> get the following error:
>
> GetVDW: no radius for atom 16 atomic number 34.
> Error termination via Lnk1e in /usr/local/chem/g09/1602.exe at Wed Jun 30
> 18:28:37 2021.
> Job cpu time: 0 days 0 hours 1 minutes 43.3 seconds.
> File lengths (MBytes): RWF= 46 Int= 0 D2E= 0 Chk= 2 Scr= 1
> Segmentation fault (core dumped)
>
> Here is my file.
>
> #HF/6-31G* SCF=tight Test Pop=MK iop(6/33=2) iop(6/42=6) opt
> # iop(6/50=1)
>
> Título
>
> 0 1
> N 0.29900 0.54000 -0.44600
> C -4.34300 0.68000 0.59300
> C -4.30200 -0.72300 0.52300
> C -3.11600 -1.39600 0.22100
> C -1.96600 -0.63600 -0.01400
> C -1.99400 0.76300 0.05700
> C -3.18900 1.42600 0.36000
> C -0.71600 1.46200 -0.21800
> C 1.61700 0.94800 -0.90400
> C 2.72600 0.42000 -0.04600
> C 2.84500 0.13700 1.28600
> C 4.19900 -0.29900 1.48600
> C 4.79900 -0.24600 0.26300
> O -0.54700 2.67600 -0.24800
> O 3.91300 0.18600 -0.68300
> Se -0.22000 -1.28300 -0.43200
> H -5.28200 1.18300 0.83100
> H -5.21100 -1.30100 0.70700
> H -3.09700 -2.48700 0.16900
> H -3.18200 2.51600 0.40400
> H 1.58500 2.05000 -0.89000
> H 1.79500 0.63300 -1.94800
> H 2.06000 0.22800 2.03300
> H 4.66100 -0.61100 2.41900
> H 5.79700 -0.47400 -0.09600
>
> Could someone help me?
>
> thankful
>
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Received on Thu Jul 01 2021 - 13:00:02 PDT
