Thank you Dr. Case.
I didnot realise that could be done. I will try and report back
Thank you again
On Sat, Nov 7, 2020 at 12:50 AM David A Case <david.case.rutgers.edu> wrote:
> 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
