VMD-L Mailing List

From: Ioana Cozmuta (ioana_at_nas.nasa.gov)
Date: Wed Feb 12 2003 - 16:52:32 CST

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
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> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> Email: johns_at_ks.uiuc.edu Phone: 217-244-3349
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>