Hi,
Thanks for providing the files.
On Tue, Nov 5, 2024 at 7:55 AM Maciej Spiegel <maciej.spiegel.umw.edu.pl> wrote:
>
> This fails and mapped.mol2 has atom names of charges.mol2, despite atommap.dat output indicates they are recognized correctly. The files:
Actually, you can see from the atommap output that you provided that
some of the atoms were not mapped:
> 35 H11 35 H
> 36 H12 36 H
> 37 H13 37 H
> --- --- 38 C
> --- --- 39 H
> --- --- 40 H
> --- --- 41 H
> 38 Cl1 42 Cl
This is because charges.mol2 contains 3 fewer atoms than A8C.pdb.
Since 'changenames' requires that all atoms have been mapped, this is
why no names are changed. Maybe I should add a flag allowing any
mapped atom names to be changed.
Also, it seems like you may have reversed the order of target and
reference to 'atommap' - do you really want A8C.pdb to be the
reference? It has generic atom names:
> HETATM 33 O 0 0.887 0.876 -0.201 O
> HETATM 34 C 0 0.046 0.947 -1.356 C
> HETATM 35 H 0 -0.762 0.254 -1.252 H
> HETATM 36 H 0 -0.345 1.939 -1.452 H
> HETATM 37 H 0 0.616 0.703 -2.228 H
which will cause problems if you try to build with it (since all atom
names in a residue must be unique).
I'll let you know if I can get around to implementing name changes
with partial atom maps. In the meantime if you know there are atoms
you do not want mapped you could always remove them from A8C.pdb to
get the atoms in target and reference to match up.
Hopefully this clears some things up.
-Dan
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Received on Thu Nov 07 2024 - 06:00:02 PST
