On Mon, Oct 30, 2017 at 1:49 PM, Diego Gomes <diego.enry.gmail.com> wrote:
> Dear all,
> I have experienced an issue with *pdb4amber* when dealing with SSBONDS
> between chains, it renumbers the atoms after handling "TER", but it doesn't
> update the CONECT record.
>
> Thankfully, *Leap* produces a warning about this wrong connection.
>
> The problem is restricted to AmberTools*17*, see bellow how to reproduce
> for *1dwc.pdb*
>
> # AmberTools 15
> source /usr/local/amber14/amber.sh
> pdb4amber -i 1dwc.pdb -o amber14.pdb
> grep "ATOM 1196" amber14.pdb
> ATOM 1196 SG CYX H 148 55.729 28.382 19.687 1.00 10.07
> S
> CONECT 24 1196
>
> # AmberTools 17
> source /usr/local/amber16/amber.sh
> pdb4amber -i 1dwc.pdb -o amber16.pdb
> grep "ATOM 1196" amber16.pdb
> ATOM 1196 CB CYX H 148 55.173 26.880 20.510 1.00 10.00
> C
> CONECT 24 1196
>
>
hi, thank you for your report.
I open an issue here to keep track:
https://github.com/Amber-MD/pdb4amber/issues/56
cheers
Hai
> --
> Diego
>
>
> --
> Prof. Diego Enry B. Gomes, PhD
> Laboratório de Biologia Computacional.
> Diretoria de Metrologia Aplicada às Ciências da Vida.
> Instituto Nacional de Metrologia, Qualidade e Tecnologia
> +55 21 2145 3262 (3265, 3070, 3075) | dgomes.pq.cnpq.br
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Received on Mon Oct 30 2017 - 20:00:03 PDT
