VMD-L Mailing List

From: Víctor (victor.gil.sepulveda_at_gmail.com)
Date: Mon Jun 15 2009 - 10:32:25 CDT

Unfortunately I have to deliver the project tomorrow so I have no much time
to explore new possibilities, but perhaps I'll give it a try in a few weeks.

Anyway, thanks for your help!

Greetings,

On Mon, Jun 15, 2009 at 5:20 PM, Axel Kohlmeyer <akohlmey_at_cmm.chem.upenn.edu
> wrote:

> 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.
>
> 

-- 
Víctor Gil Sepúlveda
E. Informatica - FIB - UPC