I am trying to run nab to create the pdb file but it isnt working (AMBER)

Here is the input file for nab:

molecule m;

m = arna( "gcuucuucuucuucgc" );

putpdb( "lr16.pdb", m, "-wwpdb -nocid -tr");

I am trying to run nab to create the pdb file with this command :

“$AMBERHOME/bin/nab lr16.nab./a.out” But it comes out saying : gcc: error: lr16.nab./a.out: No such file or directory cc failed! I have loaded the appropriate modules , please could someone help 1 Answer I have no idea about nab ... however “$AMBERHOME/bin/nab lr14.nab./a.out”


Looking at your error lr14.nab./a.out:

It suggests you didn't put a space character between lr16.nab and a.out. If you run

\$AMBERHOME/bin/nab lr14.nab ./a.out


I suspect it will work because at present it is looking for a file named lr14.nab./a.out which could be interpreted as a directory of lr14.nab. and a input file of a.out or the error suggests it is reading / as part of the file name. a.out of course doesn't exist its your specified output file name

output of ls -l

-rw-r--r-- 1 phys 89 Oct 6 12:58 lr14.nab – Peter 5 hours ago

• "/nab: lr16.nab: no such file" is what it comes up with now. This is very weird as the instructions tell me to use lr16.nab. Any ideas? – user9855 Nov 13 '20 at 0:47
• what does ls -l` give you? – M__ Nov 13 '20 at 1:52
• I will check now – user9855 Nov 13 '20 at 3:29
• -rw-r--r-- 1 phys 89 Oct 6 12:58 lr14.nab – user9855 Nov 13 '20 at 3:35
• -rw-r--r-- 1 an909 phys 145 Oct 6 12:59 README – user9855 Nov 13 '20 at 3:36