<p>Hi John,</p>
<p>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:</p>
<p>sed '/SOL/s/^ATOM /HETATM/' in.pdb</p>
<p>Hope it helps,</p>
<p>Tsjerk</p>
<p><blockquote type="cite">On Mar 20, 2012 3:50 AM, "John Ladasky" <<a href="mailto:blind.watchmaker@yahoo.com">blind.watchmaker@yahoo.com</a>> wrote:<br><br>
<div bgcolor="#FFFFFF" text="#000000">
Following up to myself:<br>
<br>
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.<br>
<br>
<a href="http://www.mail-archive.com/gmx-users@gromacs.org/msg00405.html" target="_blank">http://www.mail-archive.com/gmx-users@gromacs.org/msg00405.html</a><br>
<br>
I can hack my way around this problem. But I would still like to
understand whether, and why, I should do so.<br>
</div>
<br>--<br>
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