Re: reverting atoms introduced by name into standard PDB ones

From: Oleksiy Kovtun (okovtun_at_mrc-lmb.cam.ac.uk)
Date: Mon May 14 2018 - 07:44:15 CDT

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,
Oleksiy

> On 14 May 2018, at 13:31, Vermaas, Joshua <Joshua.Vermaas_at_nrel.gov> 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 owner-namd-l_at_ks.uiuc.edu 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: okovtun_at_mrc-lmb.cam.ac.uk

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