FAILED job on local run

DISVIS
1

Dear Responsible,

I also have experienced several failed submissions. I read some of the preceeding conversation and tried to check the chains ID to match the restrain files. Everything seems fine to me:

fixed chain is A and is first line in interaction file
scanning chain is B and is second line in interaction file

The restrain file read: B 219 CH2 A 446 CA 20.0 40.0

The current job code is: cri_3Qty7vW6

Thanks for your help,

2

CH2 is not a standard protein atom name. Why not defining it to the CA?

Or are you not looking at a protein?

Also I would define the restraint in the order of the chains, I.e. starting with chain A

3

Thanks,

I have just resubmitted the job (complete scanning) with the following corrected restrain file: A 446 CA B 219 CA 20.0 30.0
and I still get the failing message (job code cri_3QvMgY5W).

I am also using the following interaction file:
446
24 25 26 27 28 29 39 31 32 33 34 35 36 37 38 39 50 51 52 53 54 55 56 57 58 59 60 61 94 95 96 97 98 99 101 102 138 139 140 141 142 143 144 164 165 166 167 168 169 211 212 213 213 214 215 216 217 218

Fixed chain is chID A and scanning in chID B

What could I be missing?

Thanks for your help

4

It looks from the error message I could find that your input PDBs have alternate conformations of some residue.
You will need to remove those.

This can be done for example with our PDB-Tools server using the pdb_selaltloc command

5

PS: The error message is:

ValueError: Some selected interaction residues where either missing in the PDB file or had alternate conformers. Please check your input residues
and remove alternate conformers.

Make sure that all residues in your interaction list are present in the PDB file.