VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Aug 25 2003 - 19:11:16 CDT

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
  vmd_at_ks.uiuc.edu

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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