Make sure each water has consistent residue number on iits atoms, and
that each water has its own unique residue number.
Bill
On 1/9/21 6:42 AM, Eduardo R. Almeida wrote:
> Dear David A. Case,
>
> I used the symbol "..." to show that the file continues above and below the snippet that I presented in this message.
> If you want, I can also send you my PDB file, but it is big (16MB).
>
> Regarding the snippet that you asked:
>
> ATOM 69774 O WAT F9882 2.169 68.354 401.617 1.00 0.00 O
> ATOM 69775 H1 WAT F9882 2.338 68.860 402.412 1.00 0.00 H
> ATOM 69776 H2 WAT F9882 2.846 67.678 401.616 1.00 0.00 H
> TER
> ATOM 69777 O WAT F9883 32.087 33.420 403.626 1.00 0.00 O
> ATOM 69778 H1 WAT F9883 31.246 33.038 403.876 1.00 0.00 H
> ATOM 69779 H2 WAT F9883 32.206 34.155 404.228 1.00 0.00 H
> TER
> ATOM 69780 O WAT F9884 42.707 38.825 95.618 1.00 0.00 O
> ATOM 69781 H1 WAT F9884 43.617 38.571 95.468 1.00 0.00 H
> ATOM 69782 H2 WAT F9884 42.196 38.212 95.088 1.00 0.00 H
> TER
> ATOM 69783 O WAT F9885 49.632 0.133 94.110 1.00 0.00 O
> ATOM 69784 H1 WAT F9885 49.347 0.690 93.386 1.00 0.00 H
> ATOM 69785 H2 WAT F9885 50.117 0.722 94.688 1.00 0.00 H
> TER
> ATOM 69786 O WAT F9886 55.249 22.467 327.822 1.00 0.00 O
> ATOM 69787 H1 WAT F9886 55.347 21.517 327.756 1.00 0.00 H
> ATOM 69788 H2 WAT F9886 56.067 22.817 327.468 1.00 0.00 H
>
> In the warning showed by Leap, I didn't understand why it refers to a residue 19884. Also, I didn't restart counting after 9999. When I prepared my system in other program (Packmol), the initial PDB file presented this counting that I didn't change.
>
> When I saved my structure in a pdb file, I saw that the atom number goes from 1 to 99999 and the residue number goes from 1 to 9999. This is a problem for my system, because I have 190868 atoms. This way, the atom number was restarted after 99999. Consequently, I got duplicated residues, since as you said, Leaps ignores the chainids. If Leap ignores the chainids, how could I differentiate these water molecules that are duplicated?
>
> Sincerely,
>
> Eduardo.
>
>
>
>
>
>
> ________________________________
> De: David A Case <david.case.rutgers.edu>
> Enviado: sábado, 9 de janeiro de 2021 10:51
> Para: AMBER Mailing List <amber.ambermd.org>
> Assunto: Re: [AMBER] Error in xleap: water molecules
>
> On Fri, Jan 08, 2021, Eduardo R. Almeida wrote:
>> I have a system with 190868 atoms, where the majority of them are related
>> with water molecules. When I loaded this pdb file in xleap, I got the
>> following warning:
>>
>> *********************************************************
>> ...
>> -- residue 19883: duplicate [ O] atoms (total 10)
>> -- residue 19884: duplicate [ H1] atoms (total 10)
>> -- residue 19884: duplicate [ H2] atoms (total 10)
>> -- residue 19884: duplicate [ O] atoms (total 10)
>> -- residue 19885: duplicate [ H1] atoms (total 10)
>> -- residue 19885: duplicate [ H2] atoms (total 10)
>> -- residue 19885: duplicate [ O] atoms (total 10)
> Can you provide a snippet of the pdb file, around the residues listed above?
> Or around any earlier residues that give the same "10 oxygen atoms in the
> same residue" error? I'm not sure what you mean by the "..." above: showing
> the first such message is probably the most helpful. Note that residue
> 19884 for Amber is probably residue number 9884 in your PDB file, since it
> looks like you restart counting after 9999.
>
> Leap ignores chainids.
>
> ....dac
>
>
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Received on Sat Jan 09 2021 - 10:00:02 PST
