VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Fri Jun 05 2009 - 10:45:12 CDT

On Fri, 2009-06-05 at 20:44 +0530, gurunath katagi wrote:

> After obtaining the disulphide bond, i want the a pdb file of this
> complex.(protein and ligand connected by cysteine residues).
> The structure of the protein-ligand complex is not available in the
> PDB.
>
> can anybody help me in this regrad?

check out the latest VMD beta version. it contains a plugin
that would help you with this, even beyond the simple concatenation
of the two molecules. note that drawing the bond in itself does
not help much in VMD if you just save the result as a .pdb file
which contains not bonding information.

have a look at the end of this page:
http://www.ks.uiuc.edu/Research/vmd/plugins/topotools/

there is an example describe the use of "mergemols"
that you can use to combine coordinates _and_ topology
(.psf files).

and then you can use:
topo addbond
and
topo addangle
and
topot adddihedral

to add the bond/angle/dihedral definitions to make the SS bond,
and write out the combinded .pdb/.psf

cheers,
    axel.

>
> --
> Gurunath M Katagi
> M.Sc (engg) Research student
> Supercomputer Education and Research Centre
> Indian Institute Of Science
> Bangalore 

-- 
=======================================================================
Axel Kohlmeyer   akohlmey_at_cmm.chem.upenn.edu   http://www.cmm.upenn.edu
   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
=======================================================================
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