reverting atoms introduced by name into standard PDB ones

From: Oleksiy Kovtun (okovtun_at_mrc-lmb.cam.ac.uk)
Date: Mon May 14 2018 - 04:45:43 CDT

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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