Re: more than 99999 atoms in PDB files

From: LEWYN LI (
Date: Mon Dec 13 2004 - 16:53:26 CST

Dear Gilbert,

         Hi there! This is Lewyn at Columbia. Nice to "catch up" with you
at the namd-l website.

         Anyway, to answer your question: according to my experience,
"*****" is not a problem with NAMD, because, if I remember correctly, NAMD
has its own "internal" numbering system and therefore doesn't really care
about "*****".

         Just to be safe, I usually start off with a pdb file that has the
correct numbering i.e. atom 100000 and above. After a simulation, I got
pdb files with "*****", but NAMD didn't complain. So I suppose everything
is fine!

         Hope this helps.


On Mon, 13 Dec 2004, Gilbert G.Feng wrote:

> Hi,
> I am building a big system that contains more than 99999 atoms. It looks
> the pdb file is designed to record, at most, 99999 atoms. If the system is
> bigger, I got "*****" for the number of the atom. Can the NAMD
> handle this case? and how?
> Thanks
> Gilbert

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