Dear David,
thanks for suggestions. Indeed renaming GUA to LIG have been resulted in
complex without any errors.
Building topology.
Building atom parameters.
Building bond parameters.
Building angle parameters.
Building proper torsion parameters.
Building improper torsion parameters.
total 658 improper torsions applied
Building H-Bond parameters.
Incorporating Non-Bonded adjustments.
Not Marking per-residue atom chain types.
Marking per-residue atom chain types.
(Residues lacking connect0/connect1 -
these don't have chain types marked:
res total affected
CTYR 1
LIG 1
NGLU 1
)
(no restraints)
Writing pdb file: sensor_gua.pdb
Converting N-terminal residue name to PDB format: NGLU -> GLU
Converting C-terminal residue name to PDB format: CTYR -> TYR
Quit
James
2014-04-29 15:54 GMT+04:00 David A Case <case.biomaps.rutgers.edu>:
> 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 - 09:00:03 PDT
