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


2 Answers 2


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
  • $\begingroup$ "/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? $\endgroup$
    – user9855
    Commented Nov 13, 2020 at 0:47
  • $\begingroup$ what does ls -l give you? $\endgroup$
    – M__
    Commented Nov 13, 2020 at 1:52
  • $\begingroup$ I will check now $\endgroup$
    – user9855
    Commented Nov 13, 2020 at 3:29
  • $\begingroup$ -rw-r--r-- 1 phys 89 Oct 6 12:58 lr14.nab $\endgroup$
    – user9855
    Commented Nov 13, 2020 at 3:35
  • $\begingroup$ -rw-r--r-- 1 an909 phys 145 Oct 6 12:59 README $\endgroup$
    – user9855
    Commented Nov 13, 2020 at 3:36

Try this command:

$AMBERHOME/bin/nab -v lr14.nab -o ./a.out, 

then execute a.out separately using


You will get the pdb file of nab extension.


Your Answer

By clicking “Post Your Answer”, you agree to our terms of service and acknowledge you have read our privacy policy.