Error uploading pub files

usegalaxy.eu support
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21

I have tried it, still no joy

22

Good day,
I have made progress on the galaxy platform with respect to Molecular Dynamic Simulation.

However, I still have difficulty in using some tools such as RDF analysis, hydrogen bond analysis, angle analysis, dihedral analysis, ramanchandran plot.

Please kindly assist.

Thank you

23

Hi @simonbray I just wanna ask if I can run the Gromacs initial setup on a 2-chain structure? It seems I’m having the same problem, I want to study the interaction of the 2 chains together ! I tried fixing the missing residues before uploading the PDB file into Galaxy, how will this affect the simulation?

24

Hi @Marwa, we made a fix a couple of months ago to the setup tool which allows it to deal with multi-chain structures. Can you see if this is working for you?

25

@rowaiye, could you be a little more specific about the problems you encountered?

ping @tsenapathi

26

@simonbray No, I tried now to choose 1 chain only, it worked. However when I choose 2 chains out of the 4 chains it results in an error. How can I fix this?

27

@Marwa, could you share the history with me or provide more details on the error?

28

@simonbray here it is https://usegalaxy.eu/u/marwa_abdelkader/h/copy-of-gromacs-tutorial

29

Thanks for the link!

The error is not related to the multiple chains but to a problem with the PDB file. If you look at the bottom of the log file (here: https://usegalaxy.eu/datasets/11ac94870d0bb33af0b5b0844db6e950/display/?preview=True) you can see the message:

Fatal error:
Residue 293 named GLN of a molecule in the input file was mapped
to an entry in the topology database, but the atom CG used in
that entry is not found in the input file. Perhaps your atom
and/or residue naming needs to be fixed.

There is a message in the header of the PDB with this text:

REMARK 470                                                                      
REMARK 470 MISSING ATOM                                                         
REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER;           
REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER;          
REMARK 470 I=INSERTION CODE):                                                   
REMARK 470   M RES CSSEQI  ATOMS                                                
REMARK 470     GLN D 145    CG   CD   OE1  NE2

which I guess is the cause of the error. So there are some problems with the PDB that need to be fixed.

30

@simonbray thanks so much, I haven’t noticed that. It works now after I fixed it :blush:

1 Like
31

Great, glad you solved it!

Just out of interest, what tool did you use? Unfortunately we don’t have anything in Galaxy right now, hopefully that will change in the next few months.

32

I used Chimera and Modeller. Yes, it’ll be great if a tool was implemented in Galaxy to solve these issues. :blush:

33

@simonbray Dear,
i am working on protein-ligand docking and i can’t find the compound library at ChEMBL database so i choose to download pubChem , but i don’t know which function should i use to build a compound library using this tool