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
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sat Jan 09 2021 - 06:00:02 PST
