# Atom number limit for PDB file

**URL:** <https://ask.bioexcel.eu/t/atom-number-limit-for-pdb-file/1425>\
**Category:** MDWeb\
**Created:** [February 13, 2019, 1:14am UTC](https://ask.bioexcel.eu/t/atom-number-limit-for-pdb-file/1425 "2019-02-13T01:14:04Z")\
**Posts on this page:** 3\
**Page:** 1

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**Author:** ![dxzh0129](https://avatars.discourse-cdn.com/v4/letter/d/7ea924/32.png) [@dxzh0129](https://ask.bioexcel.eu/u/dxzh0129)\
**Post date:** [February 13, 2019, 1:14am UTC](https://ask.bioexcel.eu/t/atom-number-limit-for-pdb-file/1425/1 "2019-02-13T01:14:04Z")

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Hi, I am a first-time user of MDWeb. I was trying to set up a system using a symmetric protein complex made of 24000 atoms. When I try to upload the pdb, I get the error message of "PDB file exceeds maximum number of Atoms (20000)  
". I wonder what is the reason to have this atom number limit? if there is a way to get around it (eg. using symmetry?)?

Thanks in advance!

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**Author:** ![adam.hospital](https://dub1.discourse-cdn.com/flex013/user_avatar/ask.bioexcel.eu/adam.hospital/32/151_2.png) [@adam.hospital](https://ask.bioexcel.eu/u/adam.hospital)\
**Post date:** [February 18, 2019, 1:09pm UTC](https://ask.bioexcel.eu/t/atom-number-limit-for-pdb-file/1425/2 "2019-02-18T13:09:58Z")

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Hi!

MDWeb was tested for proteins with less than 20000 heavy atoms. We started to find some incompatibilities with programs used in the pre-configured workflows with larger systems. Another reason is that being a web server, it had to be restrained in the simulation length and system size.

That said, you can try to use MDWeb2, which is a version of MDWeb with added functionalities and less restrictions. But please note that this is an unstable version.

[http://mmb.irbbarcelona.org/MDWeb2/](http://mmb.irbbarcelona.org/MDWeb2/)

In BioExcel we are trying to update this idea of free MD services (at least setup + configuration files) through GUIs such as web servers. Stay tuned with BioExcel web page or subscribe to our mailing list to hear about the news!

Thanks for using our tools!

-Adam-

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**Author:** ![dxzh0129](https://avatars.discourse-cdn.com/v4/letter/d/7ea924/32.png) [@dxzh0129](https://ask.bioexcel.eu/u/dxzh0129)\
**Post date:** [February 18, 2019, 11:32pm UTC](https://ask.bioexcel.eu/t/atom-number-limit-for-pdb-file/1425/3 "2019-02-18T23:32:23Z")

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Thanks, Adam! This is very helpful information! I’ll give it a try on MDWeb2!

Cheers,  
Xiaozhe