[gmx-developers] Gromacs pdb formatting

Tsjerk Wassenaar tsjerkw at gmail.com
Mon Aug 9 22:17:35 CEST 2010


>>>>  >  But atoms in other molecules, such as water and ions should be
>>>> written
>>>>  >  in HETATM fields,
>>>>  >  not ATOM as Gromacs has always done and currently still does.

> I've always found the distinction between ATOM and HETATM very silly.

It is a bit silly. HETATM fields may make sense if there are HET,
HETNAM, HETSYN and FORMUL records, providing a sort of framework to
deal with whatever is not standard. Then again, water seems quite
standard... Do note it's not about molecules. Non-standard residues
are also designated HETATM rather than ATOM, which may result in a
protein chain (e.g. collagen, 1cag) having alternating ATOM/HETATM
sections. To do it the proper way, one should use a database of what
should be designated ATOM and what HETATM.

The question is, does it solve a problem?


Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
Groningen Institute for Biomolecular Research and Biotechnology /
University of Groningen
The Netherlands

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