RE: reverting atoms introduced by name into standard PDB ones

From: Vermaas, Joshua (
Date: Mon May 14 2018 - 07:55:45 CDT

The same sort or approach I'd imagine. I don't off-hand know what Swiss MODEL expects for the naming convention for the hydrogens, but if you want to make the error go away, you'd need to figure out what it expects for those atoms. However, these warnings might actually not be a problem. It is possible that SWISS-model will just add the missing hydrogens back in, since the hydrogens aren't included in most crystallographic pdbs anyway. The OT1 and OT2 are usually from the carboxy terminus (check with VMD! "name OT1 OT2 will probably get you two atoms at each C-terminus). For modeling purposes, it's also probably ok for those to be deleted during the modeling process.


On 2018-05-14 06:44:20-06:00 Oleksiy Kovtun wrote:

Thank you, Josh.
The aim is to have a PDB with standard atom naming since namd-inroduced atoms are not recognised by homology modelling and visualisation tools I use. This error I quoted comes from Swiss MODEL web interface.
 How do I deal with ILE,GLU and GLN ("ILE.HG11, ILE.HD1, ILE.HD2, ILE.HD3, ILE.HN, GLU.HN, GLU.OT1, GLU.OT2, GLN.HG1, GLN.HB1, GLN.HN, GLN.OT1, GLN.OT2)?

Best regards,

> On 14 May 2018, at 13:31, Vermaas, Joshua <> wrote:
> Hi Oleksiy,
> What are you trying to do, and what program generates this error message? Typically, it would probably be easiest to select the problematic atoms and rename them in VMD before rewriting your system. So something like:
> set hissel [atomselect top "resname HSD"]
> $hissel set resname HIS
> set asel [atomselect top "all"]
> $asel writepdb fewerproblems.pdb
> Would fix up your histidenes.
> -Josh
> On 2018-05-14 03:50:30-06:00 wrote:
> Dear name community,
> I have a rookie questions on how I can revert namd-generated atoms in a PDB to a standard ones.
> This is to resolve errors like this:
> Several ATOM records seem to specify unknown atoms: HSD.HD1, HSD.O, HSD.C, HSD.HD2, HSD.CD2, HSD.NE2, HSD.HE1, HSD.CE1, HSD.CG, HSD.N, HSD.ND1, HSD.HB2, HSD.HB1, HSD.CB, HSD.HA, HSD.CA, HSD.HN, ILE.HG11, ILE.HD1, ILE.HD2, ILE.HD3, ILE.HN, GLU.HN, GLU.OT1, GLU.OT2, GLN.HG1, GLN.HB1, GLN.HN, GLN.OT1, GLN.OT2 (those may be introduced by using a third party force field)., 402 ATOM records (e.g. line 15207) have unknown atoms and are deleted., Several ATOM records seem to breach IUPAC nomenclature and are translated: ILE.CD -> CD1., 32 ATOM records (e.g. line 15042) seem to breach IUPAC nomenclature and are translated.
> Many thanks,
> Oleksiy
> Dr Oleksiy Kovtun
> Research Fellow
> Briggs group
> MRC Laboratory of Molecular Biology
> Francis Crick Avenue
> Cambridge
> CB2 0QH
> UK
> Tel: + 44 1223 267551
> Email:


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