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
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Received on Tue Dec 23 2014 - 06:30:03 PST
