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

John Ladasky blind.watchmaker at yahoo.com
Mon Mar 19 19:10:49 CET 2012

I am trying to import PDB file snapshots from a GROMACS 4.5.4-generated 
trajectory into other software tools -- specifically, Biopython.  I 
generate the snapshots using trjconv in GROMACS.

I am interested in the water molecules from my solvent box, so I do not 
discard them.  When trjconv prompts me to "Select group for output", I 
select "Group 0 (System)".  However, in downstream applications, I do 
want to differentiate the solvent atoms from my protein polymer, and 
ensure that each group of atoms (protein atoms, solvent atoms) is placed 
in a distinct category.

Biopython's PDB file parser is not cooperating with me.  It is 
attempting to append the water molecules as additional RESIDUES of my 
polymer.  Obviously, this is incorrect.  So, where's the problem, 
Biopython or GROMACS?  Looking through the PDB file specification, 
version 3.2, I found the following passage:

"The ATOM records present the atomic coordinates for standard amino 
acids and nucleotides. They also present the occupancy and temperature 
factor for each atom. Non-polymer chemical coordinates use the HETATM 
record type."

If I am reading this correctly, my solvent atoms should be tagged as 
"HETATM" rather than as "ATOM".  But the files that trjconv produces 
label every atom as "ATOM", whether it's an atom from the protein or an 
atom from a water molecule.

Is there any way to make trjconv use "HETATM" for solvent atoms?  I do 
not see anything in the trjconv documentation.  I also do not understand 
why trjconv might produce PDB files which do not adhere to the 
standard.  There may be a good reason, I don't know.

Thanks for your help!

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