VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Sun Jun 14 2009 - 16:58:32 CDT

On Sun, 2009-06-14 at 22:35 +0200, Víctor wrote:
> Dear all,

dear victor,

> I have a self made protein structure with very bad positioned residues
> and then the structure is about to be disconected in some parts. I've
> noted that when i get the psf file with autopsf the on on screen
> structure seems to be fixed, but the pdb file is still the same so i
> think that the psf file is containing some kind of patches to fix the
> structure...Can I combine this psf and pdb to get a pdb file with the
> fixed structure??

what you are seeing is that the .psf file contains the information about
bonds explicitly, but the .pdb does not. if you provide a .psf file,
then VMD uses the bond information from the file, with only a .pdb
file, it has to guess. if your structure is not "good" it will guess
wrong. the best way to handle this is to either load _both_ the
.psf and the .pdb file (the .psf has no coordinate information) or
save the structure and coordinates in a different format that stores
both coodinates and topology information.

> Or maybe you know another method for fixing structures?

this is not really fixing the structure, it only changes the
bonds according to your residues from the templates that psfgen
knows. to "fix" the structure, you will have to do a geometry
optimization or something alike.

cheers,
   axel.

> Thanks in advance,
>
> --
>
> Víctor Gil Sepúlveda
> E. Informatica - FIB - UPC 

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