Atom number limit for PDB file


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!



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.

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!



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