From: Ioana Cozmuta (
Date: Mon Aug 25 2003 - 19:29:55 CDT

Hi John,

What I am actually tying to do is the following:
I have to structures: a protein and a box with water.
I want to center them in zero, align them with the z axis and remove
all the atoms from the box that overlap with the protein.
The problem is the following: if I center both structures in amber (tleap)
in zero when I view them in VMD their centers do not overlap and also
their centers is not zero anymore (although I've especially done that in
I am just curious why this difference? I wrote a code that does the
removal of the overlaping molecules, that's what I need the radii for.
I will add there the centering but then again I might want to vizualize
the centered structure and vmd may show them again shifted from each


On Mon, 25 Aug 2003, John Stone wrote:

> Dear Ioana,
> VMD reads and interprets only the PDB columns it knows how
> to make use of. As such, when writing out PDB files from VMD,
> some of the columns get default values, or are left blank,
> particularly for fields that VMD doesn't store. According to
> the PDB file spec, the last two fields of the ATOM recard
> are supposed to contain the element symbol (cols 77-78) and
> the charge (cols 79-80). Which actual fields/columns are you
> storing the radii and charge in?
> In any case, I suspect that there's no easy way for you to preserve
> the custom radii/charge info unless you were to store it in the
> occupancy and tempFactor fields, which VMD does actualy store and
> should also save.
> Since VMD isn't intended specifically to work with just PDB files,
> there are many PDB record types and fields that VMD doesn't process,
> so this is only one example of all kinds of similar limitations with PDB
> and potentially with other formats,
> Thanks,
> John Stone
> On Mon, Aug 25, 2003 at 04:24:27PM -0700, Ioana Cozmuta wrote:
> > Hi vmd users,
> >
> > I am reading in VMD a pdb file and in the last two columns of the file I
> > have the charge and radii. However after I recenter the structure and
> > select all atoms, when I write the selection into a pdb file the last two
> > columns loose the information. Is there a way to preserve the charge/radii
> > information when I write the atomselection into the pdb file?
> >
> > Thank you,
> > Ioana
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