Re: HETATM vs ATOM in .pdb file

From: Bjoern Olausson (namdlist_at_googlemail.com)
Date: Wed Aug 31 2011 - 06:20:55 CDT

On Wednesday 31 August 2011 11:56:35 Andrea Holfelder wrote:
> Hello
>
Hi, Andrea.

> Is there any major difference between HETATM and ATOM in pdb file format ?
>
You might want to read the PDB file specs:
http://deposit.rcsb.org/adit/docs/pdb_atom_format.html

> Does the solvent molecules have to be in HETATM for molecular dynamics run
> ? or it does not matter ?
>
As far as i know: NO
NAMD only takes the COORDINATES from the PDB file and IMHO it does not care
about the RECORD, but the order and name.

> Do the residues marked with HETATM behave any differently in MD simulation
> run with ATOM marked residues?
>
As far as I know: NO
Read the description for the RECORD in the PDB-file spec and you'll understand
the difference between HETATM and ATOM - HETATM it is just a "non-standard"
pool.

> Is the use of HETATM recommended for solvent molecules ?or not
> recommended?
>
It is recommended at least if you want to stick to the PDB file format... but
there are so many PDBs out there which are not conform to the specs... So if
you have no intents to share you PDB, you might do what you want with the
file, as long as your program of choice does what you expect...

I guess all your question will dissipate when reading the PDB file specs.

-- 
Bjoern Olausson
Martin-Luther-Universitšt Halle-Wittenberg 
Fachbereich Biochemie/Biotechnologie
Kurt-Mothes-Str. 3
06120 Halle/Saale
Phone: +49-345-55-24942

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