From: Axel Kohlmeyer (
Date: Wed Jan 02 2008 - 11:46:13 CST

On Wed, 2 Jan 2008, Sampo Karkola wrote:

SK> Hi,

hi sampo,

SK> I was wondering if it is possible to select atoms (or residues) from a
SK> protein based on a ligand that is not part of the protein? For example, I
SK> have a protein structure (as molecule 0) with an empty cavity and I read in
SK> a docked ligand (as molecule 1) and I would like to select protein residues

no. this is not (currently) possible. selections in VMD can only
be for a single molecule.

SK> in a 6 sphere around the ligand. If this is not possible, is there a
SK> command to merge the ligand to the protein structure?

SK> This subject might have been discussed recently on the list but I could not
SK> find it in the archives.

if you want to merge two pdb files, you can just use a text editor.
just remove the END. if you have .pdb/.psf you can use the mergepdbs
script from the script library (provided you are using the CHARMM
force field).

BTW: you can find this by sticking the following into google:

merge pdb files

restricting the search with is in general a
good way to search _all_ available resources on the TCBG servers
at the same time. ;-)


SK> Regards,
SK> Sampo
SK> ________________________
SK> Sampo Karkola
SK> Doctoral student
SK> Laboratory of Organic Chemistry
SK> Department of Chemistry
SK> POBox 55, FIN-00014
SK> University of Helsinki
SK> Finland
SK> tel. +358 9 191 50369
SK> fax. +358 9 191 50366

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.