On Sun, Oct 18, 2020, Sarah Jane wrote:
>
> I am trying to generate parameters of a docked complex using
> Amber 18 AmberTools19.I am getting the following error:Bond: Maximum
> coordination exceeded on .R<MOL 310>.A<H01 25>
The PDB file you provided looks like it is not the one you actually
used. What you attached looks like this:
HETATM 1 O MOL A 0 32.749 63.036 18.290 1.00 0.00 carn O1-
HETATM 2 O MOL A 0 33.302 63.722 16.303 1.00 0.00 carn O
HETATM 3 C MOL A 0 32.483 63.672 17.252 1.00 0.00 carn C
HETATM 4 O MOL A 0 32.543 66.789 16.533 1.00 0.00 carn O
HETATM 5 H MOL A 0 32.833 65.872 16.335 1.00 0.00 carn H
HETATM 6 O MOL A 0 31.980 69.148 17.887 1.00 0.00 carn O
HETATM 7 H MOL A 0 31.825 69.836 18.561 1.00 0.00 carn H
HETATM 8 C MOL A 0 31.265 68.568 21.980 1.00 0.00 carn C
HETATM 9 C MOL A 0 31.085 69.095 20.552 1.00 0.00 carn C
HETATM 10 C MOL A 0 31.075 64.308 17.050 1.00 0.00 carn C
HETATM 11 C MOL A 0 29.880 63.370 17.411 1.00 0.00 carn C
HETATM 12 C MOL A 0 30.876 64.528 15.521 1.00 0.00 carn C
HETATM 13 C MOL A 0 30.039 61.941 16.832 1.00 0.00 carn C
HETATM 14 C MOL A 0 30.944 63.192 14.742 1.00 0.00 carn C
HETATM 15 C MOL A 0 30.912 61.883 15.551 1.00 0.00 carn C
Here "MOL" is residue 0, and the atom names are not unique. Antechamber
can fix that for you, but you need to find out what it did, in order to
figure out which atom is "H01", etc. Also, we would need to know
exactly what commands you gave to obtain the message you cite above.
(Just saying "trying to generate parameters" is not specific enough.)
FWIW, the ligand doesn't seem to have any obvious problems.
...good luck...dac
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Oct 19 2020 - 05:00:02 PDT
