Out of memory issue while using MDweb GROMACS simulation

MDWeb
1

Thank you for the amazing program
Input pdb file was a receptor and a vaccine ligand complex of 1796 amino acids in total
After full MD setup for GROMACS, I ran it with NPT option
but it gives me an error as the one below

Type: MD_TrajectoryXTC
MD_TrajectoryXTC…
Out of memory!

Is it just due to the size of my input file?
And is it proper to use NPT option to check the stability of such input?

2

Dear SJLee,

yes, it could well be a problem related to the size of your input file.

I would recommend you to take a look at our new tools, as MDWeb is a very old infrastructure running with obsolete MD packages. I would try it with:

Hope this helps!

Thanks for using our tools!

3

Hi! I try to use BioBB server but it won’t work, I cannot submit a project. It only says uploading data when i submit my protein-ligand structure it does not go to step 2:protonation state. can you help me with this?

4

Dear gcdomingo,

we are experiencing technical problems with our computational resources behind the servers. We are working on fixing them. Please be patient and try it next week.

Thanks for your interest in our tools!