On Wed, 2014-02-26 at 10:06 -0300, Gustavo Seabra wrote:
> Hi all,
>
> I’m sort if this question has been discussed before, I admit I’ve been
> away form the developer’s community for a while…
>
> I noticed that, when trying to use the new ff12SB, the ions “Na+”, “K
> +”, etc, do not get loaded any longer. (After loading ff12SB, the
> “list” command does not show Na+, for example.)
>
> Instead, it seems that one is now able to neutralize molecules by
> adding “NA”, or “K”. My questions are:
> 1. Is this the expected behaviour?
Yes, this is expected. This change was implemented for better
compatibility with the PDB, which uses NA and K for sodium and potassium
ions, respectively.
> 2. Isn’t it going to break old LEaP scripts that use “Na+”
> explicitly?
Not if they load the ions08.lib file. The atomic_ions.lib file is the
only one with the new names (AFAICT).
> Still, (assuming the above *is* the expected behaviour) if I use NA to
> neutralize the molecule, I still have problems, due to lack of mass
> and vdW information (see below).
>
> Gustavo.
>
> ====><====
>
> > addions2 gab NA 0
[snip]
> For atom: .R<NA 500>.A<NA 1> Could not find vdW (or other) parameters for type: Na+
> For atom: .R<NA 501>.A<NA 1> Could not find vdW (or other) parameters for type: Na+
Did you source the ion parameter files? Ion parameters are no longer
loaded by default (and haven't been for some time), so you need some
type of command like:
loadAmberParams frcmod.ionsjc_tip3p
The best ion parameters are water-model dependent, so you need to load
the ones appropriate for the water model you plan to use. (You didn't
include enough of your leap input for me to see if you did this step :))
All the best,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Wed Feb 26 2014 - 05:30:04 PST
