Chain name being read as residue

[Anonymous]

Hi,

I am attempting a ligand docking run in a P450 docking both the heme cofactor and ligand simultaneously. I was able to have a successful run with just the heme group but when I attempt to add in the ligand I get an error. Currently, I’ve been getting the error “unrecognized mm_atom_type_name W” where W is the chain name for my ligand. I’ve attached my docking file, initial structure pdb file, and my options file so they can be looked at to help me resolve this issue. Thanks in advance!

[Anonymous]

First off, I believe that UNK is special cased in Rosetta. I wouldn’t use it as a three letter code. Pick some other combination of three letters instead.

But on your main issue, my guess is that you edited your params file, and in the ATOM lines where you saw “X” you changed it to “W”. That “X” wasn’t the chain letter (the chain letter does not appear at all in the params file), it was the MM AtomType designation. (“X” simply means “unspecified” — that’s fine, as for regular ligand docking you never need to consult the MM AtomType designation.) If you leave it as “X”, that should fix the error you’re getting.

[Anonymous]

That worked, thanks!

 

[Author]

Posts