[gmx-users] Trjconv PDB files define solvent as "ATOM"?

Tsjerk Wassenaar tsjerkw at gmail.com
Tue Mar 20 06:24:01 CET 2012

Hi John,

Maybe it was laziness, maybe it was the realization that the distinction
between atom and hetatm is a bit awkward that caused the developers not to
bother with it. It also doesn't relate to your problem, probably. There are
non-standard residues and covalently bound ligands that are happily part of
chains, and probably parsed correctly. Chain identifiers and ter statements
should be used to mark the polymers. Solvent should not have a chain
identifier. You can see if changing the tag helps, though:

sed '/SOL/s/^ATOM  /HETATM/' in.pdb

Hope it helps,


On Mar 20, 2012 3:50 AM, "John Ladasky" <blind.watchmaker at yahoo.com> wrote:

 Following up to myself:

Looking back through the archives, I have learned that the issue of solvent
atoms being exported from trjconv into PDB files as "ATOM" rather than as
"HETATM" is an issue that was raised fully six years ago.


I can hack my way around this problem.  But I would still like to
understand whether, and why, I should do so.

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