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

Question

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

Answer 1

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

Answer 2

Try this command:

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

then execute a.out separately using

./a.out. 

You will get the pdb file of nab extension.