Atom number limit for PDB file

MDWeb
1

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!

2

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/

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-

3

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

Cheers,
Xiaozhe