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
--
Prof Dr Renato Costa
Instituto Federal do Pará - IFPA
Grupo de Modelagem Molecular - UFPA
Tel.+55 91 985484622
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Received on Wed Jun 30 2021 - 15:00:02 PDT
