On Sat, Nov 07, 2020, Ayesha Fatima wrote:
>Created a new atom named: HT1 within residue: .R<NSER 1>
>Created a new atom named: HT2 within residue: .R<NSER 1>
>Created a new atom named: HT3 within residue: .R<NSER 1>
>Created a new atom named: HN within residue: .R<THR 2>
>Created a new atom named: HN within residue: .R<ILE 3>
Your pdb file has non-standard hydrogen names; (you don't say where this
file came from.)
Simplest fix is to use that --nohyd option in pdb4amber to remove all
the hydrogens from your pdb file. Then leap will build them back in
with the correct names. ("Correct" here means complying with
IUPAC/wwPDB standards.)
If you think the input hydrogen positions are iportant, you could also use
a text editor to change the atom names in the PDB file, but it is unlikely
that this is necessary.)
....dac
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Received on Fri Nov 06 2020 - 09:00:02 PST
