From: Peter Freddolino (petefred_at_umich.edu)
Date: Sun Jan 23 2022 - 18:26:03 CST
If I didn't know better I'd say you have duplicate bonds to atom 1. It has
two bonds to each of atoms 2-4.
(n.b. the "hydrogen group" refers to the set of hydrogens bonded to a
single heavy atom, like, say, N1...)
Best,
Peter
On Sun, Jan 23, 2022 at 7:16 PM Mare Libero <mareliber27_at_remove_yahoo.com>
wrote:
> Hello,
>
> I am trying to minimize a protein complex but I receive the error:
>
> "FATAL ERROR: Atom 1 has bad hydrogen group size. Check for duplicate
> bonds."
>
> However, when I check my psf file, atom 1 is the N-term Nitrogen, not an
> hydrogen:
>
> 29023 !NATOM
> 1 H 1 GLN N NH3 -0.300000 14.0070 0
> 2 H 1 GLN HT1 HC 0.330000 1.0080 0
> 3 H 1 GLN HT2 HC 0.330000 1.0080 0
> 4 H 1 GLN HT3 HC 0.330000 1.0080 0
> 5 H 1 GLN CA CT1 0.210000 12.0110 0
>
> 20509 !NBOND: bonds
> 1 5 2 1 2 1 3 1
> 3 1 4 1 4 1 5 6
>
>
> Any thought on what could be causing this error?
>
> Thanks in advance.
>
>
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