Hi Harmeet,
It has one line solution. I am sure, you are not loading
frcmod.ionsjc_tip3p (if you are loading TIP3P water model) file. Add
following line in your tleap:
loadamberparams frcmod.ionsjc_tip3p
Best
Kshatresh
On Tue, Dec 23, 2014 at 4:06 PM, Jason Swails <jason.swails.gmail.com>
wrote:
> On Tue, Dec 23, 2014 at 6:00 AM, Harmeet Kaur <meet.academia.gmail.com>
> wrote:
>
> > Dear Sir,
> >
> > I am unable to save the parameters of a PDB structure in tleap. The
> > structure has an overall -2 charge which was neutralized with Na+.For
> your
> > reference, I am using ff12SB force field in Amber14. It shows the
> following
> > error
> >
> > Checking Unit.
> > Building topology.
> > Building atom parameters.
> > For atom: .R<Na+ 9351>.A<Na+ 1> Could not find vdW (or other) parameters
> > for type: Na+
> > For atom: .R<Na+ 9352>.A<Na+ 1> Could not find vdW (or other) parameters
> > for type: Na+
> > Parameter file was not saved.
> >
> >
> > Kindly guide on how to trouble-shoot the error.
> >
>
> The ion parameters cannot be found. What this likely means is that you
> did not load them. The "correct" ion parameters to load depend on the
> water model you intend on using (which is why none is chosen by default).
> Googling your error message should also bring up previous discussions of
> this issue.
>
> There is a discussion of using ion parameters in the Amber 14 manual. See
> chapter 3, section 9 (on page 44) regarding the use of ions and the
> selection of a particular ion parameter set.
>
> Hope this helps,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
With best regards
************************************************************************************************
Kshatresh Dutta Dubey
Post Doctoral Researcher,
Lise Meitner Center for Computational Quantum Chemistry
Hebrew University of Jerusalem Israel
Jerusalem, Israel
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Received on Tue Dec 23 2014 - 07:00:04 PST
