[Chimera-users] Saving ligand and protein as a single PDB

Nancy nancy5villa at gmail.com
Fri Oct 2 19:24:32 PDT 2009


I am planning to run a docking simulation in a different program, and I need
to have a "reference ligand" included in the PDB file.  The particular PDB I
am working on does not have a ligand included.  So I am trying to position
one using Chimera.

I started with the protein file and a ligand file (ligand is in .mol2
format).  I loaded both into Chimera, and I correctly positioned the ligand
relative to the PDB.  I then saved both using File -> Save PDB...  I choose
to save the file relative to the protein, and I select "save multiple
models: in a single file".  However, when I load the file into the docking
program, it does not show the ligand.  Additionally, there are a few
structural errors in the output PDB file.

Please advise.


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