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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

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2 Answers 2

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

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Siba Sankar is a new contributor to this site. Take care in asking for clarification, commenting, and answering. Check out our Code of Conduct.
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