A worldwide e-Infrastructure for NMR and structural biology

Registration Issues

Help on converting regular PDF file to HADDOCK-ready file

Hi,

I am a new user. I was trying to use the HADDOCK. The ligand is an ssDNA of 22 nucleotides, with a particular secondary structure. The NMR structure is available in the PDB database. I tried to manually change the 2-letter code, such as "DT", in the original PDB file into 3-letter, such as"THY". However, the modified PDF file could not even produce the normal structure in PyMol, nor could be accepted by the HADDOCK server.

There may be a solution existing. As a new user, I would appreciate a lot if anyone could advise me what to do.

Issue status: 
Open

Error while subscribe GROMACS - Validate certificate

Hi Team,

Please find below error mail, Error message while I was trying to
 subscribe and Validate certificate under GROMACS - "My services".

Please find  attached screenshot of my certificate installed on Firefox web browser provided by IGCA since I am using this service from India. I tried flushing my browser history as directed in the error message but still validate certificate is not working.

I also have my VO membership request for VO enmr.eu has been approved.

Issue status: 
Open

Internal Server Error

Hello,

Iam submitting the restrained MD with amber port. I am getting following error.

Internal Server Error

Could you please fix this probelm as soon as possible.

Thanking you !

Issue status: 
Open

Registration issue

Hi,

I am trying to register with we-nmr to use GROMACS. I have a valid grid certificate and my vo membership request for VO enmr.eu
has been approved. However, when I try to access GROMACs under the My Services tab I get the following message when I click to validate grid certifate:

 

Internal Server Error

The server encountered an internal error or misconfiguration and was unable to complete your request.

Issue status: 
Open

HADDOCK error: TOTAL NUMBER OF DISTANCE RESTRAINTS FOR RIGID BODY DOCKING IS ZERO!

Hi Everyone,
 
I have recently started working with HADDOCK stand alone and am facing some trouble running it. I wonder if anyone of you could help me in this regard.
 
Issue status: 
Closed

Gromacs:MD simulation

User = JNU_pb;   Password=WeNMR_pb_0001; Email=biswajitch44@gmail.com

 

Dear Co-ordinator,

I want to use Gromacs for MD simulation  with a protein(transcription factor, 55 dalton) and protein-ds-oligo(5 mer) complex. Can  registration status allow me to use Gromacs without subscription.

 

 

Register with the enmr.eu VO - not possible after importing valid *.p12 certificate?

Dear WeNMR Team,
 
I have imported a personal *.p12 certificate. However, I still can't validate it.
I have cleared the browser cache before.
 
Issue status: 
Open

Fail to Subscription

Dear Members,

I am trying to subscribe the various applications/programs (GROMACS, HADDOCK) in server. Unfortunately, I cannot subscribe and following is the error keep displaying on screen. Please suggest me something to fix this issue, so that I can use the weNMR.

 

Internal Server Error

The server encountered an internal error or misconfiguration and was unable to complete your request.

Issue status: 
Open

problem faced at the time of Registration

 

Dear,

Issue status: 
Open

Cite WeNMR/WestLife

 
Usage of the WeNMR/WestLife portals should be acknowledged in any publication:
 
"The FP7 WeNMR (project# 261572) and H2020 West-Life (project# 675858) European e-Infrastructure projects are acknowledged for the use of their web portals, which make use of the EGI infrastructure and DIRAC4EGI service with the dedicated support of CESNET-MetaCloud, INFN-PADOVA, NCG-INGRID-PT, RAL-LCG2, TW-NCHC, SURFsara and NIKHEF, and the additional support of the national GRID Initiatives of Belgium, France, Italy, Germany, the Netherlands, Poland, Portugal, Spain, UK, South Africa, Malaysia, Taiwan and the US Open Science Grid."
 
And the following article describing the WeNMR portals should be cited:
Wassenaar et al. (2012). WeNMR: Structural Biology on the Grid.J. Grid. Comp., 10:743-767.

EGI-approved

The WeNMR Virtual Research Community has been the first to be officially recognized by the EGI.

European Union

WeNMR is an e-Infrastructure project funded under the 7th framework of the EU. Contract no. 261572

WestLife, the follow up project of WeNMR is a Virtual Research Environment e-Infrastructure project funded under Horizon 2020. Contract no. 675858

West-Life