# Error in PDB file on web server
**URL:** https://ask.bioexcel.eu/t/error-in-pdb-file-on-web-server/2397
**Category:** HADDOCK
**Created:** [August 14, 2020, 11:06am UTC](https://ask.bioexcel.eu/t/error-in-pdb-file-on-web-server/2397 "2020-08-14T11:06:08Z")
**Posts on this page:** 6
**Page:** 1
### Author:  [@kempc006](https://ask.bioexcel.eu/u/kempc006)
#### Post date: [August 14, 2020, 11:06am UTC](https://ask.bioexcel.eu/t/error-in-pdb-file-on-web-server/2397/1 "2020-08-14T11:06:08Z")
Hi,
I keep getting the same error when uploading my files to the web server. I was wondering what it meant?
Here’s the error:
Error in PDB file.
Issue when parsing the PDB file at line **1**.
ATOM/HETATM line does not meet the expected format
This is what my .pdb file looks like (this isn’t the whole thing, it’s quite large):
# generated by PyMOL 2.4.0
#
data\_epyc1\_R64G64\_and\_R71G71
\_entry.id epyc1\_R64G64\_and\_R71G71
#
\_cell.entry\_id epyc1\_R64G64\_and\_R71G71
\_cell.length\_a 60.585
\_cell.length\_b 60.585
\_cell.length\_c 60.585
\_cell.angle\_alpha 90.00
\_cell.angle\_beta 90.00
\_cell.angle\_gamma 90.00
\_symmetry.entry\_id epyc1\_R64G64\_and\_R71G71
\_symmetry.space\_group\_name\_H-M ‘P 1’
#
loop\_
\_atom\_site.group\_PDB
\_atom\_site.id
\_atom\_site.type\_symbol
\_atom\_site.label\_atom\_id
\_atom\_site.label\_alt\_id
\_atom\_site.label\_comp\_id
\_atom\_site.label\_asym\_id
\_atom\_site.label\_entity\_id
\_atom\_site.label\_seq\_id
\_atom\_site.pdbx\_PDB\_ins\_code
\_atom\_site.Cartn\_x
\_atom\_site.Cartn\_y
\_atom\_site.Cartn\_z
\_atom\_site.occupancy
\_atom\_site.B\_iso\_or\_equiv
\_atom\_site.pdbx\_formal\_charge
\_atom\_site.auth\_asym\_id
\_atom\_site.pdbx\_PDB\_model\_num
ATOM 1 N N . ASN . . 1 ? 22.960 31.110 32.100 1.00 0.00 0 . 1
ATOM 2 C CA . ASN . . 1 ? 23.760 32.320 31.890 1.00 0.00 0 . 1
ATOM 3 C C . ASN . . 1 ? 25.190 31.930 32.290 1.00 0.00 0 . 1
ATOM 4 O O . ASN . . 1 ? 25.580 30.900 31.750 1.00 0.00 0 . 1
ATOM 5 C CB . ASN . . 1 ? 23.100 33.510 32.610 1.00 0.00 0 . 1
ATOM 6 C CG . ASN . . 1 ? 21.710 33.800 32.010 1.00 0.00 0 . 1
ATOM 7 N ND2 . ASN . . 1 ? 21.390 35.040 31.770 1.00 0.00 0 . 1
ATOM 8 O OD1 . ASN . . 1 ? 20.920 32.910 31.740 1.00 0.00 0 . 1
ATOM 9 N N . TRP . . 2 ? 25.820 32.550 33.300 1.00 0.00 0 . 1
ATOM 10 C CA . TRP . . 2 ? 27.080 32.090 33.960 1.00 0.00 0 . 1
ATOM 11 C C . TRP . . 2 ? 27.870 30.910 33.360 1.00 0.00 0 . 1
Apologies if this seems obvious, I’m not well versed in these things.
Thank you!
---
### Author:  [@amjjbonvin](https://ask.bioexcel.eu/u/amjjbonvin)
#### Post date: [August 14, 2020, 1:02pm UTC](https://ask.bioexcel.eu/t/error-in-pdb-file-on-web-server/2397/2 "2020-08-14T13:02:39Z")
This is not a PDB format, but rather mmCIF. When saving from pymol select PDB as format.
Note that the 2.4 server should accept mmCIF.
---
### Author:  [@kempc006](https://ask.bioexcel.eu/u/kempc006)
#### Post date: [August 14, 2020, 1:16pm UTC](https://ask.bioexcel.eu/t/error-in-pdb-file-on-web-server/2397/3 "2020-08-14T13:16:30Z")
Okay, I have tried to upload both mmCIF and PDB saved from Pymol but both come back with the same error.
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### Author:  [@amjjbonvin](https://ask.bioexcel.eu/u/amjjbonvin)
#### Post date: [August 14, 2020, 1:29pm UTC](https://ask.bioexcel.eu/t/error-in-pdb-file-on-web-server/2397/4 "2020-08-14T13:29:16Z")
In which version of the server?
Can you share your PDB file?
---
### Author:  [@kempc006](https://ask.bioexcel.eu/u/kempc006)
#### Post date: [August 14, 2020, 2:19pm UTC](https://ask.bioexcel.eu/t/error-in-pdb-file-on-web-server/2397/5 "2020-08-14T14:19:54Z")
I have been using HADDOCK 2.4 web server.
I’ve managed to get it working with the pdb’s after cleaning them up
The mmCIF’s definitely aren’t working for whatever reason though.
Thank you!
---
### Author:  [@amjjbonvin](https://ask.bioexcel.eu/u/amjjbonvin)
#### Post date: [August 14, 2020, 2:36pm UTC](https://ask.bioexcel.eu/t/error-in-pdb-file-on-web-server/2397/6 "2020-08-14T14:36:46Z")
Good!
Always good practice to clean the PDBs removing any unnecessary “junk” 🙂