That's OK for acetate. Correctly protonated by MCPB's addHs.
In contrast. I encountered problems for the water molecule, which, as a
ligand at the metal, I would like to separately parameterize (i.e., treated
differently from TIP3) along the sequence of previously said codes as for
acetate.
The prep file is correct:
0 0 2
This is a remark line
molecule.res
NOH INT 0
CORRECT OMIT DU BEG
0.0000
1 DUMM DU M 0 -1 -2 0.000 .0 .0 .00000
2 DUMM DU M 1 0 -1 1.449 .0 .0 .00000
3 DUMM DU M 2 1 0 1.522 111.1 .0 .00000
4 O oh M 3 2 1 1.540 111.208 -180.000 -0.785000
5 H1 ho E 4 3 2 0.960 108.657 81.398 0.392000
6 H2 ho E 4 3 2 0.960 83.119 -159.226 0.392000
LOOP
and atom types are what I wish.
The xlm library descending from this prep file is read by MCPB' addHs,
telling that
for NOH 0 bonds added (like for TIP3 waters "HOH", which however becomes
protonated)
residue: NOH in NOH: failed to build atoms.
In fact, contrary to acetate, NOH's "O" atom was not protonated.
Should perhaps the atoms in NOH.pdb used for antechamber be called
differently from water atoms: O H1 H2? Or what else?
thanks for help
francesco
On Mon, Dec 8, 2014 at 4:18 AM, Jason Swails <jason.swails.gmail.com> wrote:
>
> > On Dec 7, 2014, at 4:47 PM, Francesco Pietra <chiendarret.gmail.com>
> wrote:
> >
> > Perhaps
> >
> > antechamber resid.pdb -> resid.prep
> >
> > parmchk resid.prep -> frcmod
> >
> > prep2xml *-resid.prep -> resid.xml
> >
> > frcmod2xml frcmod -> frcmod.xml
> >
> >
> >
> > unless experts can suggests something better.
>
> That’s what I would do. In fact, that’s why I think those programs are
> there in the first place.
>
> All the best,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Dec 08 2014 - 08:30:02 PST
