On Tue, Apr 29, 2014, James Starlight wrote:
>
> Then I've parametrize my ligand following tutorial obtaining cGMP for its
> deprotonated (-1) form
> antechamber -i ligand.pdb -fi pdb -o ligand.mol2 -fo mol2 -c bcc -s 2 -nc -1
>
> > check GUA
If "GUA" is cGMP, try giving it a different residue name. I think you are
seeing the effects of Amber thinking that GUA is the old name for what is now
called DG.
You could also edit your leaprc file (or a copy of it) to remove the aliasing
of GUA to DG. The alias is there to try to help people with old-style (PDB
version 2) PDB files.
> FATAL: Atom .R<DG3 207>.A<O2' 35> does not have a type.
My guess(!?!) is that the DG3 comes originally from GUA, as described above.
> Here you can see that new oxygen have been added to the last protein's TYR
> aa
That looks correct: you have a TER card following the TYR, which Amber takes
to mean that the TYR should have a carboxylate group at the end.
>
> Created a new atom named: O2' within residue: .R<DG3 207>
Same problem as above. Of course, deoxy-guanine won't have an O2' atom,
and LEaP gets confused.
I'm guessing some here, but it's certainly worth a try to change the residue
names.
...dac
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Received on Tue Apr 29 2014 - 05:00:02 PDT
