VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri Apr 11 2003 - 14:55:44 CDT

Ioana,
  This sounds odd, can you send me (or provide via FTP/web) a copy
of the files you're referring to here? I'd like to determine why
you get the odd structure when you use the prmtop file. It might
be something simple..

Thanks,
  John Stone
  vmd_at_ks.uiuc.edu

On Thu, Apr 10, 2003 at 05:52:25PM -0700, Ioana Cozmuta wrote:
>
> Hi John,
>
> I am using amber prmtop/prmcrd files in namd (and not charmm)
> If I load the prmtop file and then on top of it the prmcrd file I get some
> weird structure. If I use ambpdb to generate a pdb file out of the
> prmtop/prmcrd files and then load the structure in vmd, everything looks
> fine. This structure is the initial one in the dynamics so it should be
> identical to the first frame in the trajectory file.
> The weird thing is that the initial pdb file has a center in zero (0,0,0)
> and when I calculate the center of the shifted frame it is zero too just
> that it shows shifted on the screen
>
> I will try to load the prmtop first and then the dcd without loading the
> prmcrd. maybe this will work.
>
> Thanks,
> Ioana
>
> On Thu, 10 Apr 2003, John Stone wrote:
>
> >
> > Ioana,
> > Do the coordinates in your DCD file differ substantially from those
> > contained in the PDB file you loaded? You can skip loading the PDB and
> > instead load the PSF file and then I would expect this to go away
> > since VMD will just use the coordinates from the DCD file then.
> > (If you load a PDB, then VMD loads the coordinates from the PDB
> > as the first coordinate set, subsequent DCD loads just add additional
> > frames. If you load a PSF, then VMD will only use the coordinates
> > it finds in the DCD, but gets the bonding info from the PSF file...)
> >
> > John Stone
> > vmd_at_ks.uiuc.edu
> >
> >
> > On Thu, Apr 10, 2003 at 05:00:42PM -0700, Ioana Cozmuta wrote:
> > > Hi,
> > >
> > > There is something strange happening in VMD with my water box. I load the
> > > pdb file and it is centered in zero in the center of my screen as well,
> > > Then I load the namd generated dcd file and the first frame already
> > > shifts my whole water box into the left corner of the screen. If I
> > > calculate for this frame what is the center of the box it says zero.
> > > Any idea why this happens and how I could get around it?
> > > THanks a lot,
> > > Ioana
> >
> > --
> > 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