RE: reverting atoms introduced by name into standard PDB ones

From: Vermaas, Joshua (
Date: Mon May 14 2018 - 07:31:44 CDT

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.


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,

Dr Oleksiy Kovtun
Research Fellow
Briggs group
MRC Laboratory of Molecular Biology
Francis Crick Avenue

Tel: + 44 1223 267551

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