VMD-L Mailing List

From: Justin Gullingsrud (justin_at_ks.uiuc.edu)
Date: Wed Apr 03 2002 - 10:46:09 CST

Hi,

One strange thing about your pdb files is that many of the waters exactly
overlap. This is what's confusing VMD's bond generation code. VMD is simply
trying to bond atoms that are near each other, so when molecules overlap you
get a plethora of extraneous bonds. I would suggest removing duplicate waters
first. Also, if you can build a structure file to specify the bonds
explicitly, you won't have to rely on VMD's admittedly fallible bond search
code.

Cheers,

Justin
 

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
> > 

-- 
Justin Gullingsrud      3111 Beckman Institute
H: (217) 384-4220       I got a million ideas that I ain't even rocked yet...
W: (217) 244-8946       -- Mike D