hi again,
the script does work as expected. The index you saw did not reflect the
atom index.
I've check with ParmEd.
pdb4amber -i 1dwc --pdbid -o at17.pdb
In [1]: import parmed as pmd
In [2]: x = pmd.load_file('./at17.pdb')
In [3]: x.atoms[1195] # NOTE: I used 1195 instead of 1196 since parmed use
0-based index while the one reported in pdb CONECT use 1-based index.
Out[3]: <Atom SG [1195]; In CYX 147>
In [4]: x.atoms[23] # use 0-based index
Out[4]: <Atom SG [23]; In CYX 3>
Which reflect the "CONECT 24 1196" # use 1-based index
PS: If you see the at17.pdb content, you can see something like
ATOM 2354 N GLN I 298 38.581 11.502 -4.835 1.00 33.77
N
TER 2355 GLN I 298
FYI about TER:
https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/pdbintro.html
Hai
On Mon, Oct 30, 2017 at 10:46 PM, Hai Nguyen <nhai.qn.gmail.com> wrote:
>
>
> 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
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Oct 30 2017 - 20:30:02 PDT
