Can't cut column in Linux

Question 1

This is because there are multiple spaces and cut can just handle them one by one.

You can start from the 5th position:

$ cut -d' ' -f 1,5- file
ATOM HD13 ILE   206       9.900  15.310  13.450  0.0196 1.4870
ATOM  C   ILE   206      10.870  16.560  17.500  0.8343 1.9080
ATOM  OXT ILE   206      11.780  15.734  17.425 -0.8190 1.6612
ATOM  O   ILE   206       9.929  16.225  18.095 -0.8190 1.6612

Or squeeze spaces with tr -s like below (multiple spaces will be lost, though):

$ tr -s ' ' < file | cut -d' ' -f1,3,4,5,6,7,8,9,10
ATOM HD13 ILE 206 9.900 15.310 13.450 0.0196 1.4870
ATOM C ILE 206 10.870 16.560 17.500 0.8343 1.9080
ATOM OXT ILE 206 11.780 15.734 17.425 -0.8190 1.6612
ATOM O ILE 206 9.929 16.225 18.095 -0.8190 1.6612

Note you can indicate from 3 to the end with 3-:

tr -s ' ' < file | cut -d' ' -f1,3-

In fact I would use awk for this:

awk '{$2=""; print}' file

or just

awk '{$2=""} 1' file

Question 2

There are many spaces in your file. So, you've to start with number of spaces.

The new.txt contains

ATOM   3197 HD13 ILE   206       9.900  15.310  13.450  0.0196 1.4870
ATOM   3198  C   ILE   206      10.870  16.560  17.500  0.8343 1.9080
ATOM   3199  OXT ILE   206      11.780  15.734  17.425 -0.8190 1.6612
ATOM   3200  O   ILE   206       9.929  16.225  18.095 -0.8190 1.6612

and this is the command to print second column

root@52:/home/ubuntu# cut -d' ' -f4 new.txt

3197
3198
3199
3200

where -d stands for delimiter i.e 'space' in this case denoted by ' '

However, awk comes pretty handy in such cases

**# awk '{print $2}' new.txt**

Question 3

You can select the position of the content in the first row at that column (3197) and then select the string at the same position in all rows with awk:

cat filename | awk -v field="3197" 'NR==1 {c = index($0,field)} {print substr($0,c,length(field))}'

souce: https://unix.stackexchange.com/a/491770/20661