Re: [AMBER] amber pdb > 100,000 atoms

From: David A Case <>
Date: Fri, 12 Aug 2016 08:42:19 -0400

On Fri, Aug 12, 2016, Neha Gandhi wrote:
> I have a biphasic system with > 1000000 atoms and the obvious problem is
> pdb files can support numbering upto 99,999 atoms. Is there a way to load
> files in tleap other than pdb or mol2 format?
> When I save pdb file in chimera, it will save atoms > 99999 as ****. AMBER
> will complain about duplicate numbering. Programs like Discovery studio
> don't even allow saving such a big pdb file. Most programs will prefer
> mmCif format. How do I get around working with this issue in tleap?

What version of AmberTools are you using? When you say, "AMBER will complain
about duplicate numbering", what do you mean? Which program are you running,
and what does the complaint say?

tleap pretty much ignores atom numbers when loading a pdb file. You might
try just changing all the "****" to a number like 1, and see what happens.
I'd also recommend asking the chimera mailing list if there are options in
chimera to handle large strutures in a different way. (The Chimera folks
are exceedingly good at responding to user input.)

[Aside: the notion that "most programs" prefer mmcif is not true in my
experience. Amber should probably do better in this respect, but we
routinely read and write pdb files with more than 100,000 atoms, so the
urgency has not been there....]


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Received on Fri Aug 12 2016 - 06:00:06 PDT
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