VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Apr 03 2002 - 10:45:40 CST

Dear Phuong,
  It works fine for me, though without a PSF file you are getting
bad bonds due to having a structure with overlapping atoms.

I did this to load the structure files as an animation:
  animatepdbs animatepdbs 1 2 "xxx_%d.pdb"

That loads both of the xxx_1.pdb and xxx_2.pdb files into VMD,
the first one as the main structure file (from which bond determination
is done) and the second as an additional coordinate frame.

To avoid the bad bonds, you'll either need to make a PSF topology file
or you'll need to choose an initial frame that doesn't have your
water atoms overlapping each other, which is what is tripping up
the distance based bond search code. One of these two options will
cure the bond problem for you.

Let us know if you have other questions,

  John Stone
  vmd_at_ks.uiuc.edu

On Wed, Apr 03, 2002 at 06:20:54PM +0200, Nguyen Hoang Phuong wrote:
>
> Dear Stone,
>
> I have tried with two ways: Using your script file animatepdbs or
> concatenate all of the PDB files into one file (with END between
> them). Unfortunately, both methods don't work. I attach here the two pdb
> files.
>
> Regards,
>
> Phuong
>
>
> >
> > Dear Phuong,
> > How are you loading your collection of PDB files into VMD?
> > If you concatenate all of the PDB files into one file, with
> > "END" marks between them, you should be able to get VMD to
> > read the concatenated PDB file as a trajectory. If you have
> > any strange bonds in your structure when loading just the PDB,
> > the best course of action is to supply VMD with a topology file
> > such as a PSF file, so that it doesn't have to guess the bonds
> > with a distance based search. You can create a PSF file with the
> > standalone 'psfgen' program that comes with NAMD, or with the
> > psfgen package that was included as part of the VMD 1.7.1 release
> > for several of the supported VMD platforms. Alternately, you can
> > use other programs like X-PLOR or Charmm to do this.
> >
> > Let us know if you have more questions.
> >
> > Thanks,
> > John Stone
> > vmd_at_ks.uiuc.edu
> >
> > On Wed, Apr 03, 2002 at 01:24:16PM +0200, Nguyen Hoang Phuong wrote:
> > >
> > > Dear VMD Users,
> > >
> > > I would like to animate the colection of the pdb files but VMD draws the
> > > strange bonds between water molecules. For each pdb file, everything is
> > > fine. Does anyone have the experience about this? Thanks in advance.
> > >
> > > Phuong
> >
> > --
> > NIH Resource for Macromolecular Modeling and Bioinformatics
> > Beckman Institute for Advanced Science and Technology
> > University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> > Email: johns_at_ks.uiuc.edu Phone: 217-244-3349
> > WWW: http://www.ks.uiuc.edu/~johns/ Fax: 217-244-6078
> > 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349              
  WWW: http://www.ks.uiuc.edu/~johns/      Fax: 217-244-6078