VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Mon Jun 15 2009 - 10:20:28 CDT

On Mon, 2009-06-15 at 09:21 +0200, Víctor wrote:
> Thanks Axel.

victor,

> What I really want is to do this kind of "fixing" ( just getting some
> kind of more relaxed structure, because i'm working an iterative
> modelling algorithm).

VMD is not a modeling tool and thus is completely indifferent to
whatever coordinates you feed it. it doesn't do any changes to
coordinates unless you program them (via script).

> I've tried wit minimization fixing CA or N atoms with NAMD, but as
> they need also the psf files I need to process them. As the structure
> is somewhat chaotic in some points, psfgen tries to patch it where
> there is no need (for me) and it creates too many segments when I just

as of recent beta versions of VMD there is an alternate way to build
connectivity (i.e. what you need to write a .psf file). if you know
exactly which bonds you need and which angles, dihedrals, etc. or
if you have a template .psf file which just needs some modifications
then you could try using the topotools plugin for that. let me know
if you need help.

cheers,
   axel.

> want to have one (my single chain segment). Would it be possible to
> tell psfgen not to apply any patch? (i've read the u.g. and it seems
> it's impossible, isn't it?
>
> Regards,
>
> On Sun, Jun 14, 2009 at 11:58 PM, Axel Kohlmeyer
> <akohlmey_at_cmm.chem.upenn.edu> wrote:
> 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.
>
>
>
>
> --
>
> 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.