Dear sir,
Thank you so much, its working now.
Sincerely,
Shilpa T
On Thu, Sep 6, 2018 at 6:26 PM Jason Swails <jason.swails.gmail.com> wrote:
> On Thu, Sep 6, 2018 at 8:20 AM Sushi Shilpa <sushishilpa.gmail.com> wrote:
>
> > Dear Amber users,
> >
> > I am trying to create topology and coordinate files for the protein which
> > contains Arsenic. I am following 126-LJ non bonded tutorial. I am using
> > AMBER 16 and AmberTools 17.
> > Here is the tleap.in file
> > source leaprc.protein.ff14SB
> > source leaprc.gaff
>
> source leaprc.water.spce
> > loadamberparams frcmod.ions1lm_126_tip3p
> > loadamberparams fcrmod.ionsjc_tip3p
> >
>
> Why are you using the SPCE water model, but ions parametrized for the TIP3P
> model? You should be using the ion parameters corresponding to the water
> model you actually plan to use.
>
> Also, these two frcmod files are *different* ion parameters created by
> different groups with different philosophies on which properties to fit
> to. You should pick one or the other, but not both. What happens in this
> case is that the parameters from the second overwrites the parameters from
> the first.
>
> loadoff atomic_ions.lib
> > AS = loadmol2 AS.mol2
> > mol = loadpdb ArsD120_AS_initial_sele.pdb
> > solvatebox mol SPCBOX 8
> > addions mol Na+ 0
> > savepdb mol As_ArsD.pdb
> > saveamberparm mol As_ArsD.prmtop As_ArsD.inpcrd
> > quit
> >
> >
> > I have loaded the mol2 file but still I am getting an error mentioned
> > below.
> > For atom: .R<AS 121>.A<AS 1> Could not find vdW (or other) parameters for
> > type: AS
> >
>
> The mol2 file is not enough. That's the residue template that provides a
> mapping of atoms within residues to specific atom types. You still need to
> load parameter files (e.g. parm.dat or frcmod files) that contain
> parameters for the atom types defined within the residue templates (like
> the mol2).
>
> You can use antechamber to generate a mol2 file for the atoms within
> AS.mol2.
>
> HTH,
> Jason
>
> --
> Jason M. Swails
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Received on Fri Sep 07 2018 - 02:00:01 PDT
