VMD-L Mailing List

From: David Norris (danorris_at_ks.uiuc.edu)
Date: Fri May 26 2000 - 09:51:19 CDT

>
> This might be a likely place to ask this. Is there such a thing as a
> valid PDB file containing 100000 atoms or more? According to the
> format docs the atom serial number field is only 5 digits. Any
> suggestions about the best way to handle this are welcome.
>
> Keith Refson
>

Hello,

   Different MD packages have different solutions to this problem. XPLOR,
for example, starts using letters for the most significant digit - ie.
'A0000' becomes 10000. This extension allows up to 260,000 atoms in a
single file.

   In VMD, though, the serial number field of PDB files is actually
ignored, and VMD uses its own numbering system instead for internal use.
So t would not cause a problem for these serial numbers to repeat. Thus
if you need for some reason to fit more than 260,000 atoms in one PDB
file, you could just set all the serial numbers to 0, or start
renumbering from 0 at 260,000, or any number of possibilities.. This
might cause problem in other MD packages as it's not standard, but it
should allow you to get your system into VMD.

Thanks for using VMD!

David Norris
vmd_at_ks.uiuc.edu