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.
Dr Oleksiy Kovtun
MRC Laboratory of Molecular Biology
Francis Crick Avenue
Tel: + 44 1223 267551
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