1

I am trying to execute a perl script from Ubuntu (14.04 LTS). The script is transOutput.pl which calls an executable pdb_trans. However, when I run the script, I get the following error that pdb_trans is not found - see below.

toni@toni-ThinkPad-S3-S440:~/Desktop/PatchDock$ perl transOutput.pl output.txt 1 10

Ligand PDB: 7RSA.pdb

Receptor PDB: 2BNH.pdb

/home/toni/Desktop/PatchDock/pdb_trans  -0.04513 -0.08622 2.50522 50.82232 33.24094 -17.12692 < 7RSA.pdb >> output.txt.1.pdb

sh: 1: /home/toni/Desktop/PatchDock/pdb_trans: not found

Does anyone have any ideas? Thanks.

ankit7540
  • 4,185
Antoni Borysik
  • 469
  • 3
    can you please [edit] your question and include the output of ls -l /home/toni/Desktop/PatchDock/pdb_trans ? – Wayne_Yux May 04 '16 at 12:20
  • Is there executable /home/toni/Desktop/PatchDock/pdb_trans in place? – Ho1 May 04 '16 at 12:29
  • 1
    And what does the title have to do with the body? – Rinzwind May 04 '16 at 12:52
  • toni@toni-ThinkPad-S3-S440:~/Desktop/PatchDock$ ls -l /home/toni/Desktop/PatchDock/pdb_trans -rwxr-xr-x 1 toni toni 353707 Aug 18 2004 /home/toni/Desktop/PatchDock/pdb_trans – Antoni Borysik May 08 '16 at 14:51
  • Assuming that you are using this package PatchDock, according to the readme file it seems that you will need to add the PatchDock directory to your path. Did you do that? – hkdtam May 10 '16 at 05:17

1 Answers1

2

Your perl script is trying to execute pdb_trans and it is using "sh"

Likely you've already worked around this issue, but see this answer on U&L.

It appears that the executable, which you reported in comments above as being present can't find the dynamic libraries it needs to load

GAD3R
  • 3,507
David Dyck
  • 78
  • 7