VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Feb 13 2003 - 14:13:58 CST

Dear Ioana,
  Do your files contain box information? If so, you'll need to use
the "crdbox" type instead of "crd". If that doesn't solve the problem,
then send me a note (no need for all of VMD-L) and if possible I'd like
to get a copy of the file that gives you problems.

Thanks,
  John Stone
  vmd_at_ks.uiuc.edu

On Wed, Feb 12, 2003 at 02:52:32PM -0800, Ioana Cozmuta wrote:
> Hi John,
>
> When I load the pdb file everything seems fine in my structure except that
> the terminal Hydrogens do not show bonded to the neighboring oxygen atoms.
> When I load first the .prmcrd file using the crd type in vmd and also the
> .prmtop with parm7 type something goes wrong as the structure shows like
> having a huge bond between one of the hydrogens and the oxygen. I looked
> into the file and things look all right.
> i do not have a trajectory file it is just a simple initial structure.
> Is this the correct way to load the structure?
>
> Thanks,
> Ioana
>
> On Wed, 12 Feb 2003, John Stone wrote:
>
> >
> > Dear Ioana,
> > If you're loading the structure from a PDB, VMD is forced to guess
> > what atoms are bonded to each other. If it guesses incorrectly, the
> > best solution is to load the actual AMBER Parm file rather than a PDB
> > version of the same structure, as VMD will get the full connectivity
> > information from the Parm file where it will not from a PDB.
> > Let us know if you need more help with this. I assume you're using
> > VMD 1.8 right?
> >
> > Thanks,
> > John Stone
> > vmd_at_ks.uiuc.edu
> >
> > On Wed, Feb 12, 2003 at 02:03:29PM -0800, Ioana Cozmuta wrote:
> > > Hi,
> > >
> > > I have an RNA single strand, hydrogen terminated generated with amber.
> > > When I load the file in vmd however the terminal hydrogens are not
> > > recognized as being bonded to the neighboring oxygen atoms.
> > > Any idea why this is happening and what is the best way to correct this?
> > >
> > > Thank you,
> > > Ioana
> > >
> > >
> > > ****************************************************************************
> > > * Ioana Cozmuta, PhD * *
> > > * NASA-AMES Research Center * "Gravitation can not be held responsible*
> > > * Mail Stop 230-3 * for people falling in love" *
> > > * Moffet Field,CA 94035 * *
> > > * phone: (650) 604-0993 * Albert Einstein*
> > > * fax: (650) 604-0350 * (1879-1955) *
> > > ****************************************************************************
> >
> > --
> > 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