From: Axel Kohlmeyer (
Date: Mon Jan 12 2009 - 08:54:21 CST

On Mon, 12 Jan 2009, Shirin Awasthi wrote:

SA> hi.

hi sirin.

SA> i have a protein and a ligand which i have already docked into it
SA> using GOLD v3.2 both load as separate files in the VMD window. my
SA> problem is how to complex them together so that the output i have is
SA> a single pdb file comprising the protein and transformed ligand
SA> coordinates docked into it. is there any command to do this?

a text editor?? just remove the END tag from the first molecule and
adapt or remove whatever header lines the second molecule contains.

whether the result is what you need depends a lot on what you intend
to do with it. for example, if you want to start a simulation from
the complex, you will need to build a topology file and if you want
to this with psfgen, the you actually have to keep them separate.



Axel Kohlmeyer
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
If you make something idiot-proof, the universe creates a better idiot.