VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Thu May 03 2007 - 16:01:46 CDT

On Fri, 4 May 2007, kong.winter wrote:

KW> Hi all,
KW>
KW> I'm eager to know how to conect two proteins with VMD.

please check out the various tutorials on VMD.

- you can use psfgen to merge different segments to one large psf file.

- you can use RMSD alignment to align structures

- you can use selections to write out parts of a file
  (so they can be reconnected)

other than that, you can always contact the authors
of the paper you refer to, in case they have used
special scripts etc...

this is certainly not an automatic process.

cheers,
   axel.

KW>
KW> A new paper (Eileen Puklin-Faucher et al., JCB 2006) said that:
KW> The crystal structures of the ¦Áv¦Â3 integrin in complex with an RGD-containing mimetic ligand (Protein Data Bank [PDB] code 1L5G) and of FNIII10 from the FNIII7-10 tetramer (PDB code 1FNF) were adopted to build the FNIII10¨C¦Áv¦Â3 starting structure with the program VMD (Humphrey et al., 1996).
KW>
KW> Step 1: the RGD tripeptides of the two separate structures were aligned
KW> Step 2: then the mimetic ligand from the ¦Áv¦Â3 structure was removed
KW>
KW> How to do the two steps above in VMD ?
KW> Any tips are appreciated,
KW> thank you very much!
KW>
KW> KD
KW>
KW>
KW>
KW>
KW> kong.winter
KW> 2007-05-04
KW> 

-- 
=======================================================================
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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If you make something idiot-proof, the universe creates a better idiot.