The HADDOCK category is meant to discuss any HADDOCK-related issue. For general information about HADDOCK refer to HADDOCK – Bonvin Lab
Hi, I want to renumber the atom sequentially like H, H1, H2 etc. I tried pdb tools function Pdb_uniquename and pdb_reres but it deletes almost all atoms and my ligand becomes fragmented. What should I do? I have attached the orginal pdb file and pdb file after using pdb tools. Please suggest.
pdb_uniquename should do the trick.
No need for pdb_reres
The pdb_uniquename returns the pdb file by deleting all repetitive atoms. Ligand is fragmented in the output. How can I correct this?
Can you share your ligand file?
Are you using the PDB-tools pdb_uniqname tool (or some other tool called pdb_uniquename)?
I just tested pdb_uniqname and it is working fine, not deleting atoms…
Hi, Thank you for sending through the pdb file.
How did you change this? I have several ligands that I need to edit in the same way
simply using a local installation of pdb-tools (https://github.com/haddocking/pdb-tools)
and with as command:
pdb_uniqname NH1.pdb >NH1-renamed.pdb
is there any way to do this using the web based pdb tools? The installation instructions says python is required and I have no idea about it.
I just checked the server and it seems it is filtering similar atom names within one residue, which is not happening at the command line level. This is coming from biopython used in the server.
I opened an issue about it, but don’t know when it will be solved.
If you are going to do a lot of modelling, it is worth investing time to learn about Linux and command line
