<p>I would like to use the python wrapper for packmol (MDAPackmol) for my research. In order to do so, I have tried to work with the example code and pdb files provided on <a href="https://github.com/MDAnalysis/MDAPackmol" rel="nofollow noreferrer">GitHub</a> so I can gain an understanding of the how to use the wrapper. However, when I run the code, I receive the following error message: <code>ValueError: invalid literal for int() with base 10: '' </code>.</p>
<p>Here is the complete trace back.</p>
<p><a href="https://i.sstatic.net/Sa41Z.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/Sa41Z.png" alt="" /></a></p>
<p>The error originates at <code>start.resname</code> being a zero-length string. It seems to be a problem with the resname having a number and a letter and thus is a problem with <code>Universe</code> (the object returned by <code>load_packmol_output</code>). Thus, there is a problem with the residues. Any advice or insight would be greatly appreciated. Thanks!</p>

CC BY-SA 4.0
2020-07-07T18:03:29.800Z
H @bioinf99 thanks for your post. The error is simple the parser is expecting an integer and not getting one. Tracing it on the information given, is not going to be easy. The location doesn't help much. It ain't packmol thats the problem. Maybe someone here has used the wrapper ... It could lots of things ...I ain't optimistic here, but lets see. My best guess is its the 'argparse' command and you're not entering what it wants to see. In that case you'd need to look at the opening code. If that doesn't mean much to you I'd contact the developers. Just my views however.
M__
CC BY-SA 4.0
2020-07-07T18:07:52.483Z
Thanks for your reply. I agree with your assessment. I have looked at the source code but am unsure about making changes directly to it. Unfortunately, I have emailed the developer, but he has not answered.
bioinf99
CC BY-SA 4.0
2020-07-07T18:12:52.960Z
You'd need to send it through an IDE with breakpoints (or at least that's how I'd do it, to look at all the variables and their parsing to the package) and thats lots of work. Someone on here might know, or the developer might be on site. Consider Snakemake if this doesn't work out?? Snakemake is well supported (I don't use it BTW)..
M__
CC BY-SA 4.0
2020-07-07T18:20:02.613Z
Thanks for the ideas. Definitely will look into it if there isn't an easier solution.
bioinf99
CC BY-SA 4.0
2020-07-08T08:54:11.413Z
One thing worth checking is if test files provided crash similarly. Also, about the email radio silence, a package with 7 stars could be one that is not really intended for the general public. An alternative is raising issues on GitHub —I for one answer those quicker as watchers get notified too and is public.
Matteo Ferla
CC BY-SA 4.0
2020-07-08T14:52:27.370Z
Thank you for your comment. The test file does not appear to produce any errors. Thank you for your insight regarding raising the issues on GitHub. My lab really wants this to work.
bioinf99
CC BY-SA 4.0
2020-07-09T07:06:03.017Z
Sorry, I just re-read your Q and I think you've inadvertently misdirected everyone. The first arrow points at the function/class call not at a specific argument. The error is from `start.resname` being a zero-length string —not sure why resname is a letter + number. It is a property of the `Universe` object returned by `load_packmol_output`. So the packmol call seems to have worked, but the residues have some oddity. So you might want to alter your Q...
Matteo Ferla
CC BY-SA 4.0
2020-07-09T12:41:35.363Z
Thanks. So don't worry about the instructions? That would make sense, because it is what was shown in the documentation. It's actually a problem with MDAnalysis? Thanks again.
bioinf99
CC BY-SA 4.0
2020-07-09T13:07:20.170Z
Sorry for another question, but I am new to working through these types of errors. I was wondering how you knew it started at `start.resname`. Thanks!
bioinf99
<python><computational-biochemistry><cheminformatics>
Question about Using MDAPackmol (packmol in python)
# Question about Using MDAPackmol (packmol in python)

(Asked by: username_0 on 2020-07-07)

I would like to use the python wrapper for packmol (MDAPackmol) for my research. In order to do so, I have tried to work with the example code and pdb files provided on [GitHub](https://github.com/MDAnalysis/MDAPackmol) so I can gain an understanding of the how to use the wrapper. However, when I run the code, I receive the following error message: `ValueError: invalid literal for int() with base 10: ''` .

Here is the complete trace back.

[![](https://i.sstatic.net/Sa41Z.png)](https://i.sstatic.net/Sa41Z.png)

The error originates at `start.resname` being a zero-length string. It seems to be a problem with the resname having a number and a letter and thus is a problem with `Universe` (the object returned by `load_packmol_output`). Thus, there is a problem with the residues. Any advice or insight would be greatly appreciated. Thanks!

**Tags:** python, computational-biochemistry, cheminformatics
> **Comments:**
> **username_1**: H @bioinf99 thanks for your post. The error is simple the parser is expecting an integer and not getting one. Tracing it on the information given, is not going to be easy. The location doesn't help much. It ain't packmol thats the problem. Maybe someone here has used the wrapper ... It could lots of things ...I ain't optimistic here, but lets see. My best guess is its the 'argparse' command and you're not entering what it wants to see. In that case you'd need to look at the opening code. If that doesn't mean much to you I'd contact the developers. Just my views however.  
> **username_0**: Thanks for your reply. I agree with your assessment. I have looked at the source code but am unsure about making changes directly to it. Unfortunately, I have emailed the developer, but he has not answered.  
> **username_1**: You'd need to send it through an IDE with breakpoints (or at least that's how I'd do it, to look at all the variables and their parsing to the package) and thats lots of work. Someone on here might know, or the developer might be on site. Consider Snakemake if this doesn't work out?? Snakemake is well supported (I don't use it BTW)..  
> **username_0**: Thanks for the ideas. Definitely will look into it if there isn't an easier solution.  
> **username_2**: One thing worth checking is if test files provided crash similarly. Also, about the email radio silence, a package with 7 stars could be one that is not really intended for the general public. An alternative is raising issues on GitHub —I for one answer those quicker as watchers get notified too and is public.  
> **username_0**: Thank you for your comment. The test file does not appear to produce any errors. Thank you for your insight regarding raising the issues on GitHub. My lab really wants this to work.  
> **username_2**: Sorry, I just re-read your Q and I think you've inadvertently misdirected everyone. The first arrow points at the function/class call not at a specific argument. The error is from `start.resname` being a zero-length string —not sure why resname is a letter + number. It is a property of the `Universe` object returned by `load_packmol_output`. So the packmol call seems to have worked, but the residues have some oddity. So you might want to alter your Q...  
> **username_0**: Thanks. So don't worry about the instructions? That would make sense, because it is what was shown in the documentation. It's actually a problem with MDAnalysis? Thanks again.  
> **username_0**: Sorry for another question, but I am new to working through these types of errors. I was wondering how you knew it started at `start.resname`. Thanks!  

---

## 0 answers

