A worldwide e-Infrastructure for NMR and structural biology

AMBER Issues

Internal Server Error

Hello, I

am 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

AMBER - results download impossible

Hi,
I'm not able anymore to download the results of my AMBER calculations.
An internal server error occurs each time I try to retrieve my data.
Could you please fix this issue ?
Thanks a lot.
Marc QUINTERNET

Issue status: 
Open

PMEMD 14 does not support this NMR refinement option. - Please use sander 14 instead.

Dear AMBER support team
I would like to run AMBER for Structure refinement using Restrained Molecular Dynamics (RMD) with the AMBER package by using pdb file , dihedral angle file , hbond.upl and hbond.lol  file.

 

Before that I wanted to check the run with example files which you gave for the structure 2KT0. (Tutorial)

I submitted the calculation by using GPU Grid.

After a few minutes the calculation was finished.

Issue status: 
Open

Amber : server is down

Hello wenmr support team,

I sumbitted the job to amber and it is showing as internal server problem.

Please fix the problem as soon as possible.

Issue status: 
Open

AMPS down

Hi,

It seems that the AMPS portal is down.

I tried to submit some calculations this morning but it failed.

Since noon, it's no longer possible  to access the main web page.

Would you please make the server accessible once again.

Thanks a lot.

Marc

 

Issue status: 
Open

Access to the web page and Lot of crash

Hi,

Since few days, I have real difficulties to access the AMPS-NMR web page (http://py-enmr.cerm.unifi.it/access/index).

Moreover, over my last 100 calculations, only 15 finsihed properly. All the rest crashes immediatly after the "S" stage.

These kinds of problem were absent last months.

Have you stablity problems at the moment ?

Thanks for answering.

Marc

 

Issue status: 
Open

Can't submit job

Dear Amber support team,

 

I am trying to submit a job over wenmr, but the job won't go through. It looks like the server is not responding.

 

Best regards,

Andras Boeszoermenyi

Issue status: 
Open

Some Basic explanation on weNMR usage

Hi All, and happy new year.

I was triyng  to run MD calculation on this server but I did not succed. My last submitted job (number ID= 1387225616) run for a couple of weeks and then stopped without generating any, even partial, output, despite having NTPR set to =500. I believe some basic infos regarding the sever usage will be very helpful to me.

My most impelling question is: 

Issue status: 
Open

No trajectory file generated from a run?

 

 

Issue status: 
Open

Cd ions in protein cluster

Dear WeNMR users and professionals.

I was trying to perform Amber simulation on Cyana 2.1 calculated structure. There I have two Cd coordinated by 6 cysteine residues. I got several problems with recognishion of atom types.

1) Cysteine. CYM and CYSS are not recognized. Should I download a topology file? When I was trying to make topology file using antechamber and downloaded CYSS.pdb (just copied from cyana library) it didn't work and topology file looked like this:

RESI MOL
GROUP
end

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