# Error message - inconsistency in your data

**URL:** <https://ask.bioexcel.eu/t/error-message-inconsistency-in-your-data/4156>\
**Category:** HADDOCK\
**Created:** [March 6, 2023, 9:15am UTC](https://ask.bioexcel.eu/t/error-message-inconsistency-in-your-data/4156 "2023-03-06T09:15:51Z")\
**Posts on this page:** 3\
**Page:** 1

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**Author:** ![mecovai](https://avatars.discourse-cdn.com/v4/letter/m/d9b06d/32.png) [@mecovai](https://ask.bioexcel.eu/u/mecovai)\
**Post date:** [March 6, 2023, 9:15am UTC](https://ask.bioexcel.eu/t/error-message-inconsistency-in-your-data/4156/1 "2023-03-06T09:15:51Z")

</div>

Hi, I have a trouble with protein-protein interaction, I am always receiving email with Error message - inconsistency in your data type of:  
Second pdb file contains multiple forms of the same residue. This is not supported in the current form - I looked at it but all atoms were unique… I tried to edit it.

Than I receive Error message:  
The second PDB has no ATOM lines with the specified chain(s)

or Error message:  
Second pdb file is incorrectly formatted. Please align the columns of your PDB properly.

I honestly don’t know how to correct the PDB file (I am editing it in PSPad).  
There appears to be always mistake.

Downloaded PDB file:

 ![image](https://europe1.discourse-cdn.com/flex013/uploads/bioexcel/original/1X/1d2da88c5d7b56b322f053f8904d59fdcf98bf54.png)

Edited PDB file:

 ![image](https://europe1.discourse-cdn.com/flex013/uploads/bioexcel/original/1X/74c3294cb3c716e192fcf9063ba2d839cc4b5ac2.png)

I honestly don’t know what to do with it.

Thanks a lot for any advise,  
Best regards,  
Mirka

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<div class="post-metadata">

**Author:** ![honoratorv](https://dub1.discourse-cdn.com/flex013/user_avatar/ask.bioexcel.eu/honoratorv/32/672_2.png) [@honoratorv](https://ask.bioexcel.eu/u/honoratorv)\
**Post date:** [March 6, 2023, 12:52pm UTC](https://ask.bioexcel.eu/t/error-message-inconsistency-in-your-data/4156/2 "2023-03-06T12:52:33Z")

</div>

Looking at your screenshots I’m assuming you are trying to use `1cll`, check the output below with [`pdb-tools`](https://www.bonvinlab.org/pdb-tools/);

```plaintext
$ pdb_fetch 1cll > 1cll.pdb
$ cat 1cll.pdb | grep ATOM | pdb_selaltloc > 1cll_fixed.pdb
$ diff 1cll.pdb 1cll_fixed.pdb | grep ATOM
< ATOM 896 CG AASP A 118 32.107 2.291 -1.516 0.50 13.30 C
< ATOM 897 CG BASP A 118 31.758 0.438 -0.326 0.50 22.66 C
< ATOM 898 OD1AASP A 118 31.940 2.877 -0.421 0.50 16.97 O
< ATOM 899 OD1BASP A 118 30.962 0.421 0.650 0.50 22.97 O
< ATOM 900 OD2AASP A 118 32.863 2.737 -2.402 0.50 16.23 O
< ATOM 901 OD2BASP A 118 32.886 -0.103 -0.173 0.50 22.16 O
# ...
> ATOM 896 CG ASP A 118 32.107 2.291 -1.516 0.50 13.30 C
> ATOM 898 OD1 ASP A 118 31.940 2.877 -0.421 0.50 16.97 O
> ATOM 900 OD2 ASP A 118 32.863 2.737 -2.402 0.50 16.23 O

```

So it seems like your residue 118 should be:

```plaintext
ATOM 891 N ASP A 118 29.174 -0.150 -1.906 1.00 10.98 N
ATOM 892 CA ASP A 118 29.839 1.168 -1.812 1.00 10.40 C
ATOM 893 C ASP A 118 29.437 2.041 -3.014 1.00 13.14 C
ATOM 894 O ASP A 118 29.249 3.263 -2.842 1.00 16.62 O
ATOM 895 CB ASP A 118 31.348 1.000 -1.697 1.00 16.46 C
ATOM 896 CG ASP A 118 32.107 2.291 -1.516 0.50 13.30 C
ATOM 898 OD1 ASP A 118 31.940 2.877 -0.421 0.50 16.97 O
ATOM 900 OD2 ASP A 118 32.863 2.737 -2.402 0.50 16.23 O

```

Could you try using the snippet above and see if you can make the submission?

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<div class="post-metadata">

**Author:** ![amjjbonvin](https://dub1.discourse-cdn.com/flex013/user_avatar/ask.bioexcel.eu/amjjbonvin/32/23_2.png) [@amjjbonvin](https://ask.bioexcel.eu/u/amjjbonvin)\
**Post date:** [March 6, 2023, 5:44pm UTC](https://ask.bioexcel.eu/t/error-message-inconsistency-in-your-data/4156/3 "2023-03-06T17:44:22Z")

</div>

If you look at the screenshot you sent, you will see instances of AASP and BASP for residue 118.

This is a case where several side-chains conformations are seen in the crystal structure. You need to select only one of those.  
This can be done with our PDB-tools server using the pdb\_selaltloc command.

[https://bianca.science.uu.nl/pdbtools/manual#pdb\_selaltloc](https://bianca.science.uu.nl/pdbtools/manual#pdb_selaltloc)