I don't think this is about your ligand, the messages indicate it is about
atom names on the HIE residues. did you process the pdb somehow after
taking it from Amber? The names don't match what Amber would have used. You
should not have HD1 atoms on the HIE residues.
On Thu, Oct 8, 2020 at 3:29 PM Jatin Kashyap <jk435.njit.edu> wrote:
> Dear AMBER Community,
>
> I am facing an error[1] while performing complex parametrization step, as
> described in the antechamber tutorial(
> https://ambermd.org/tutorials/basic/tutorial4b/index.html).
> I had faced this error before as well, and it got solved after I edit the
> complex PDB file manually to make sure the ligand atom names are the same
> as that in ligand.mol2 file.
>
> But in this case, I checked multiple times about making sure the ligand's
> atom names, and they are the same but still I am getting this error. As
> there are more than 100 ligand atoms and I don't know any other method than
> to verify the names manually. Can anybody please help me fix this, is there
> any other reason that could contribute to this error?
>
> Thank you very much.
>
>
> [1]
>
> > complex = loadpdb complex4.pdb
> Loading PDB file: ./complex4.pdb
> -- residue 512: duplicate [ H] atoms (total 2)
> -- residue 263: duplicate [ H] atoms (total 2)
> -- residue 781: duplicate [ H] atoms (total 2)
> -- residue 527: duplicate [ H] atoms (total 2)
> -- residue 283: duplicate [ H] atoms (total 2)
> -- residue 284: duplicate [ H] atoms (total 2)
> -- residue 287: duplicate [ H] atoms (total 2)
> -- residue 555: duplicate [ H] atoms (total 2)
> -- residue 304: duplicate [ H] atoms (total 2)
> -- residue 818: duplicate [ H] atoms (total 2)
> -- residue 567: duplicate [ H] atoms (total 2)
> -- residue 569: duplicate [ H] atoms (total 2)
> -- residue 317: duplicate [ H] atoms (total 2)
> -- residue 584: duplicate [ H] atoms (total 2)
> -- residue 592: duplicate [ H] atoms (total 2)
> -- residue 345: duplicate [ H] atoms (total 2)
> -- residue 601: duplicate [ H] atoms (total 2)
> -- residue 602: duplicate [ H] atoms (total 2)
> -- residue 353: duplicate [ H] atoms (total 2)
> -- residue 354: duplicate [ H] atoms (total 2)
> -- residue 612: duplicate [ H] atoms (total 2)
> -- residue 371: duplicate [ H] atoms (total 2)
> -- residue 629: duplicate [ H] atoms (total 2)
> -- residue 149: duplicate [ H] atoms (total 2)
> -- residue 156: duplicate [ H] atoms (total 2)
> -- residue 159: duplicate [ H] atoms (total 2)
> -- residue 674: duplicate [ H] atoms (total 2)
> -- residue 421: duplicate [ H] atoms (total 2)
> -- residue 679: duplicate [ H] atoms (total 2)
> -- residue 175: duplicate [ H] atoms (total 2)
> -- residue 688: duplicate [ H] atoms (total 2)
> -- residue 692: duplicate [ H] atoms (total 2)
> -- residue 438: duplicate [ H] atoms (total 2)
> -- residue 440: duplicate [ H] atoms (total 2)
> -- residue 698: duplicate [ H] atoms (total 2)
> -- residue 704: duplicate [ H] atoms (total 2)
> -- residue 715: duplicate [ H] atoms (total 2)
> -- residue 469: duplicate [ H] atoms (total 2)
> -- residue 734: duplicate [ H] atoms (total 2)
> -- residue 481: duplicate [ H] atoms (total 2)
> -- residue 484: duplicate [ H] atoms (total 2)
> -- residue 238: duplicate [ H] atoms (total 2)
> -- residue 498: duplicate [ H] atoms (total 2)
> -- residue 755: duplicate [ H] atoms (total 2)
> -- residue 245: duplicate [ H] atoms (total 2)
>
> Warning: Atom names in each residue should be unique.
> (Same-name atoms are handled by using the first
> occurrence and by ignoring the rest.
> Frequently duplicate atom names stem from alternate
> conformations in the PDB file.)
>
> Created a new atom named: HD1 within residue: .R<HIE 36>
> Created a new atom named: HD1 within residue: .R<HIE 53>
> Created a new atom named: HD1 within residue: .R<HIE 176>
> Created a new atom named: HD1 within residue: .R<HIE 229>
> Created a new atom named: HD1 within residue: .R<HIE 267>
> Created a new atom named: HD1 within residue: .R<HIE 301>
> Created a new atom named: HD1 within residue: .R<HIE 533>
> Created a new atom named: HD1 within residue: .R<HIE 570>
> Created a new atom named: HD1 within residue: .R<HIE 645>
> Created a new atom named: HD1 within residue: .R<HIE 672>
> Created a new atom named: HD1 within residue: .R<HIE 730>
> Created a new atom named: HD1 within residue: .R<HIE 736>
> Created a new atom named: HD1 within residue: .R<HIE 812>
> Created a new atom named: HD1 within residue: .R<HIE 833>
> total atoms in file: 8317
> Leap added 5082 missing atoms according to residue templates:
> 5082 H / lone pairs
> The file contained 14 atoms not in residue templates
> >
>
>
>
>
> ——
> Jatin Kashyap
> Ph.D. Student
> Department of Mechanical and Industrial Engineering
> New Jersey Institute of Technology (NJIT)
> University Heights
> Newark, NJ 07102-1982
> Phone- (201)889-5783
> Email- jk435.njit.edu
>
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Received on Thu Oct 08 2020 - 13:00:02 PDT
