I am trying to run nab to create the pdb file but it isn`t working (AMBER) Here is the input file for nab:
molecule m;
m = arna( &quot;gcuucuucuucuucgc&quot; );
putpdb( &quot;lr16.pdb&quot;, m, &quot;-wwpdb -nocid -tr&quot;);
I am trying to run nab to create the pdb file with this command :
“$AMBERHOME/bin/nab lr16.nab./a.out”
But it comes out saying :
gcc: error: lr16.nab./a.out: No such file or directory
cc failed!
I have loaded the appropriate modules , please could someone help
I have no idea about nab ... however
“$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