Re: HETATM vs ATOM in .pdb file

From: Axel Kohlmeyer (
Date: Wed Aug 31 2011 - 06:16:16 CDT

On Aug 31, 2011, at 6:03 AM, Andrea Holfelder <>


Is there any major difference between HETATM and ATOM in pdb file format ?

Yes. The PDB standard defines which atoms have to be labeled with ATOM
(basically all atoms in known biopolymer residues) and everything else is a

Does the solvent molecules have to be in HETATM for molecular dynamics run ?


or it does not matter.?


Do the residues marked with HETATM behave any differently in MD simulation
run with ATOM marked residues?

No. The behavior is determined by the force field.

Is the use of HETATM recommended for solvent molecules ?or not recommended?

All MD codes I know are completely ignorant with respect to this issue.

Do you have any indication to believe differently?


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