Answers.Body: <p>thanks! I figured out the solution, it was the cns. I downloaded the binaries instead of compiling from source and it works!</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2019-09-12T10:12:06.527Z
Answers.Text: Thanks for posting your solution! But please ask a new question for the follow-up question. This site is not a forum, so we don't do discussions, only questions and answers. You might want to take the [tour] or visit our [help] to understand more. In the mean time, I have removed the question from this answer, but please feel free to ask it as a new question.
Answers.UserDisplayName: terdon
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2019-09-12T08:15:58.890Z
Answers.LastActivityDate: 2019-09-12T10:12:16.683Z
Answers.LastEditDate: 2019-09-12T10:12:16.683Z
Answers.UserDisplayName: DanielSebas
Answers.Body: <p>The <code>target</code> variable, which is set to the first part of the sequence file name, should be <code>sequence</code> according to your given command line. However the error message thinks it is <code>c600m2-tail-before-lysin-sequence</code>. Have you edited the command line for simplicity?</p>
  
  <p>I'm a little worried about the floating point errors, which are almost certainly from CNS as there are 3 CNS calls and the error shows up 3 times. I would test your CNS installation to see if everything is okay - maybe try some examples from <a href="https://www.mrc-lmb.cam.ac.uk/public/xtal/doc/cns/cns_1.3/getting_started/frame.html" rel="nofollow noreferrer">their website</a>. An error there would explain why no output is generated.</p>
  
  <p>You can ignore any errors below line 5 of the above program output for now, as they are follow-on errors. In particular the question title isn't the 'real' error here, the real error is that no PDB files are generated on <a href="https://github.com/psipred/DMPfold/blob/master/run_dmpfold.sh#L160" rel="nofollow noreferrer">line 160</a>.</p>
  
  <p>By the way, I wouldn't use <code>10 500</code> as parameters for iteration number and number of models. It will take ages to run. I'd just use the defaults (omit the arguments), which we find gives good results.</p>
  
  <p>Finally, I'll point out that the <a href="https://github.com/psipred/DMPfold" rel="nofollow noreferrer">DMPfold repository</a> has an issue tracker where you can raise any future issues. Though we may as well finish debugging this one here since we've started!</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2019-09-12T10:17:51.083Z
Answers.Text: Ok, I cant ask more questions on this thread as stated by the person below. So, I will be asking next questions in another thread with title "DMPfold: is it suitable to get 5000 models to compare with rosetta".
Answers.UserDisplayName: DanielSebas
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2019-09-11T22:14:48.747Z
Answers.LastActivityDate: 2019-09-11T22:14:48.747Z
Answers.UserDisplayName: jgreener
Body: <p>I am running DMPfold, "seq2maps.sh" ran successfully, but whrn running "run_dmpfold.sh", it gives me this error:</p>
  
  <pre><code>   Note: The following floating-point exceptions are signalling: IEEE_UNDERFLOW_FLAG IEEE_DENORMAL
  Note: The following floating-point exceptions are signalling: IEEE_UNDERFLOW_FLAG IEEE_DENORMAL
  seed =  30603
  Note: The following floating-point exceptions are signalling: IEEE_UNDERFLOW_FLAG IEEE_DENORMAL
  /media/Deepak/NPRP10/softwares/dmpfold/DMPfold-master/run_dmpfold.sh: line 177: c600m2-tail-before-lysin-sequence_[1-9]*.pdb: No such file or directory
  No atoms read from PDB file
  0 models read from PDB file
  Outliers:
  
  
  Traceback (most recent call last):
    File "/media/Deepak/NPRP10/softwares/dmpfold/DMPfold-master/nn/dmp-softmax/pytorch_dmp_iterdistpred_cb.py", line 82, in &lt;module&gt;
      main()
    File "/media/Deepak/NPRP10/softwares/dmpfold/DMPfold-master/nn/dmp-softmax/pytorch_dmp_iterdistpred_cb.py", line 55, in main
      with open(sys.argv[3], 'r') as refpdbfile:
  FileNotFoundError: [Errno 2] No such file or directory: 'best_qdope.pdb'
  Traceback (most recent call last):
    File "/media/Deepak/NPRP10/softwares/dmpfold/DMPfold-master/nn/dmp-hb/pytorch_iterdmp_hbpred.py", line 75, in &lt;module&gt;
      main()
    File "/media/Deepak/NPRP10/softwares/dmpfold/DMPfold-master/nn/dmp-hb/pytorch_iterdmp_hbpred.py", line 53, in main
      with open(sys.argv[3], 'r') as refpdbfile:
  FileNotFoundError: [Errno 2] No such file or directory: 'best_qdope.pdb'
  No valid current contacts.
  </code></pre>
  
  <p>Can you please let me know how this can be solved? </p>
  
  <p>the comand line is:</p>
  
  <pre><code>run_dmpfold.sh sequence.fasta sequence.21c sequence.map ./dmpfold-lysin 10 500 &amp;&gt; dmpfold-log.log
  </code></pre>
  
  <p>Thanks!</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2019-09-11T15:41:32.937Z
Comments.Text: Please [edit] your question and show us line 177 of `/media/Deepak/NPRP10/softwares/dmpfold/DMPfold-master/run_dmpfold.sh`. As you can see in the error message, the script is looking for files named `c600m2-tail-before-lysin-sequence_[1-9]*.pdb` and it is doing so on line 177. What is this script? Where did you get it? Could it have hard-coded input files? All of your errors are about missing files.
Comments.UserDisplayName: terdon
Tags: <protein-structure>
Title: Dmpfold error "No such file or directory: 'best_qdope.pdb'" when running "run_dmpfold.sh"?
ThreadText: # Dmpfold error "No such file or directory: 'best_qdope.pdb'" when running "run_dmpfold.sh"?
  
  (Asked by: username_0 on 2019-09-11)
  
  I am running DMPfold, "seq2maps.sh" ran successfully, but whrn running "run\_dmpfold.sh", it gives me this error:
  
  ```
     Note: The following floating-point exceptions are signalling: IEEE_UNDERFLOW_FLAG IEEE_DENORMAL
  Note: The following floating-point exceptions are signalling: IEEE_UNDERFLOW_FLAG IEEE_DENORMAL
  seed =  30603
  Note: The following floating-point exceptions are signalling: IEEE_UNDERFLOW_FLAG IEEE_DENORMAL
  /media/Deepak/NPRP10/softwares/dmpfold/DMPfold-master/run_dmpfold.sh: line 177: c600m2-tail-before-lysin-sequence_[1-9]*.pdb: No such file or directory
  No atoms read from PDB file
  0 models read from PDB file
  Outliers:
  
  Traceback (most recent call last):
    File "/media/Deepak/NPRP10/softwares/dmpfold/DMPfold-master/nn/dmp-softmax/pytorch_dmp_iterdistpred_cb.py", line 82, in <module>
      main()
    File "/media/Deepak/NPRP10/softwares/dmpfold/DMPfold-master/nn/dmp-softmax/pytorch_dmp_iterdistpred_cb.py", line 55, in main
      with open(sys.argv[3], 'r') as refpdbfile:
  FileNotFoundError: [Errno 2] No such file or directory: 'best_qdope.pdb'
  Traceback (most recent call last):
    File "/media/Deepak/NPRP10/softwares/dmpfold/DMPfold-master/nn/dmp-hb/pytorch_iterdmp_hbpred.py", line 75, in <module>
      main()
    File "/media/Deepak/NPRP10/softwares/dmpfold/DMPfold-master/nn/dmp-hb/pytorch_iterdmp_hbpred.py", line 53, in main
      with open(sys.argv[3], 'r') as refpdbfile:
  FileNotFoundError: [Errno 2] No such file or directory: 'best_qdope.pdb'
  No valid current contacts.
  
  ```
  
  Can you please let me know how this can be solved?
  
  the comand line is:
  
  ```
  run_dmpfold.sh sequence.fasta sequence.21c sequence.map ./dmpfold-lysin 10 500 &> dmpfold-log.log
  
  ```
  
  Thanks!
  
  **Tags:** protein-structure
  
  > **Comments:**
  > **username_1**: Please [edit] your question and show us line 177 of `/media/Deepak/NPRP10/softwares/dmpfold/DMPfold-master/run_dmpfold.sh`. As you can see in the error message, the script is looking for files named `c600m2-tail-before-lysin-sequence_[1-9]*.pdb` and it is doing so on line 177. What is this script? Where did you get it? Could it have hard-coded input files? All of your errors are about missing files.  
  
  ---
  
  ## 2 answers
  
  ### Answer by username_2 on 2019-09-11. Score: 1
  
  The `target` variable, which is set to the first part of the sequence file name, should be `sequence` according to your given command line. However the error message thinks it is `c600m2-tail-before-lysin-sequence`. Have you edited the command line for simplicity?
  
  I'm a little worried about the floating point errors, which are almost certainly from CNS as there are 3 CNS calls and the error shows up 3 times. I would test your CNS installation to see if everything is okay - maybe try some examples from [their website](https://www.mrc-lmb.cam.ac.uk/public/xtal/doc/cns/cns_1.3/getting_started/frame.html). An error there would explain why no output is generated.
  
  You can ignore any errors below line 5 of the above program output for now, as they are follow-on errors. In particular the question title isn't the 'real' error here, the real error is that no PDB files are generated on [line 160](https://github.com/psipred/DMPfold/blob/master/run_dmpfold.sh#L160).
  
  By the way, I wouldn't use `10 500` as parameters for iteration number and number of models. It will take ages to run. I'd just use the defaults (omit the arguments), which we find gives good results.
  
  Finally, I'll point out that the [DMPfold repository](https://github.com/psipred/DMPfold) has an issue tracker where you can raise any future issues. Though we may as well finish debugging this one here since we've started!
  
  > **Comments:**
  > **username_0**: Ok, I cant ask more questions on this thread as stated by the person below. So, I will be asking next questions in another thread with title "DMPfold: is it suitable to get 5000 models to compare with rosetta".  
  
  ---
  
  ### Answer by username_0 on 2019-09-12. Score: 0
  
  thanks! I figured out the solution, it was the cns. I downloaded the binaries instead of compiling from source and it works!
  
  > **Comments:**
  > **username_1**: Thanks for posting your solution! But please ask a new question for the follow-up question. This site is not a forum, so we don't do discussions, only questions and answers. You might want to take the [tour] or visit our [help] to understand more. In the mean time, I have removed the question from this answer, but please feel free to ask it as a new question.  
  
  ---
  
  