Hello! I am new with MDWeb simulations. I have started my project and uploaded a PDB file with the category Base Structure. The program did not give the chance to check structure checkings. I tried to download my project files clicking on this URL: http://mmb.irbbarcelona.org/MDWeb/userData/dump/aliathan _MDWeb5d5acbee0daa7.MDWebDump.tgz
but this 404 Not Found error appeared and this message: The requested URL /MDWeb/userData/dump/aliathan _MDWeb5d5acbee0daa7.MDWebDump.tgz was not found on this server.
Apache/2.2.8 (Ubuntu) PHP/5.2.4-2ubuntu5.14 with Suhosin-Patch mod_perl/2.0.3 Perl/v5.8.8 Server at mmb3.mmb.pcb.ub.es Port 80
Any help could be great! Thank you so much in advance!
Hi!
This link is generated when trying to download the whole MDWeb project and is only available for 24h. I’m not able to reproduce the error in my side.
Can I ask you what are you trying to do with MDWeb? Run a MD simulation? Run a MD setup? I strongly recommend you to take a look at the tutorial available here:
http://mmb.irbbarcelona.org/MDWeb//help.php?id=tutorial
Thanks for using our tool!
Regards,
-Adam-
Dear Adam! Thank you so much for the reply.
I am trying to use the MDWeb to simulate the binding reaction of a Transcription Factor with its DNA binding site. I am not sure If this is possible. I have registered at MDWeb and tried for starters to simulate a base structure for the NF-kappaB p65 protein. But I didn’t get very fur because of this error.
Thank you again for your help!
Hi,
MDWeb is designed to be an entry point for the ones starting with Molecular Dynamics simulations. I’m afraid studying the binding reaction of a protein-DNA complex is far from its possibilities. But anyway, you should be able to prepare the NF-kappaB p65 protein to run a MD simulation with it. Please, try to follow the steps described in the MD setup tutorial, and get back to us if you find any problems.
Thanks again for your interest in our tool!
Regards,
-Adam-
Ok I see. Thank you so much again! Could you suggest a way to study the binding reaction with a similar approach? I am afraid I am new with molecular dynamics and I am not familiar with the tools.
Thank you for your time and support!
You can take a look at the Umbrella Sampling tutorial for GROMACS:
http://www.mdtutorials.com/gmx/umbrella/index.html
Hope it helps!
