text: user-1: 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
  
  user3848: 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
  
  
  user15929: 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.
  
original_text: -1: <p>Here is the input file for nab:</p>
  <pre><code>molecule m;
  m = arna( &quot;gcuucuucuucuucgc&quot; );
  putpdb( &quot;lr16.pdb&quot;, m, &quot;-wwpdb -nocid -tr&quot;);
  </code></pre>
  <p>I am trying to run nab to create the pdb file with this command :</p>
  <pre><code>$AMBERHOME/bin/nab lr16.nab\./a.out
  </code></pre>
  <p>But it comes out saying :</p>
  <pre><code>gcc: error: lr16.nab./a.out: No such file or directory
  cc failed!
  </code></pre>
  <p>I have loaded the appropriate modules , please could someone help</p>
   3848: <p>I have no idea about <code>nab</code> ... however</p>
  <pre><code>“$AMBERHOME/bin/nab lr14.nab./a.out”
  </code></pre>
  <p>Looking at your error <code>lr14.nab./a.out:</code></p>
  <p>It suggests you didn't put a space character between <code>lr16.nab</code> and <code>a.out</code>. If you run</p>
  <pre><code>$AMBERHOME/bin/nab lr14.nab ./a.out
  </code></pre>
  <p>I suspect it will work because at present it is looking for a file named lr14.nab./a.out which could be interpreted as a directory of <code>lr14.nab.</code> and a input file of <code>a.out</code> or the error suggests it is reading <code>/</code> as part of the file name. <code>a.out</code> of course doesn't exist its your specified output file name</p>
  <hr />
  <p>output of <code>ls -l</code></p>
  <pre><code>-rw-r--r-- 1 phys 89 Oct 6 12:58 lr14.nab – Peter 5 hours ago
  </code></pre>
   15929: <p>Try this command:</p>
  <pre><code>$AMBERHOME/bin/nab -v lr14.nab -o ./a.out, 
  </code></pre>
  <p>then execute a.out separately using</p>
  <pre><code>./a.out. 
  </code></pre>
  <p>You will get the <code>pdb</code> file of nab extension.</p>
  