This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Save Union Of Protein Plus Ligand As A Pdb-Like Molecule

I have a PDB of some protein (without ligand), converted to mol2 format, and a mol2 file of a ligand. I would like to have a new file that consists of the union of two molecules, in PDB or mol2 format. I tried to get this with Pymol, so I created a selection of both molecules and saved it, but it is not recognized as a good PDB for the input in Discovery Studio. So I would need a way to create this kind of union of molecules but in a format similar to the one that appears on the PDB database for proteins crystallized with ligands, any hints?

protein
• 4,796 views • link
updated by João Rodrigues João Rodrigues • written by Flow Flow

ok, the solution is to open both files with pymol; and then without creating any selection, just use save file.pdb, and the two molecules are correctly stored in the new pdb file

• 0 views • link
written by Flow Flow

1 answer

Well, you can easily copy and paste the ligand coordinates at the bottom of the protein PDB file. As long as the residue numbers don't overlap, it's fine.

Otherwise, can you put it somewhere so we can see exactly where the problem might be? Pastebin or so should do the trick.

• 0 views • link
written by João Rodrigues João Rodrigues

it does not work for me, by the way, I have found the solution

• 0 views • link
written by Flow Flow

It has to work, because that is essentially what PyMOL just did. But glad you managed!

• 0 views • link
written by João Rodrigues João Rodrigues

Log in to answer this question.

More posts like this