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 - 07:00:06 PST
