Re: [AMBER-Developers] Ions parameters in ff12SB

From: Gustavo Seabra <>
Date: Wed, 26 Feb 2014 10:28:50 -0300

Thanks Jason,

On Feb 26, 2014, at 10:14 AM, Jason Swails <> wrote:

> 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 :))

No, I did *not* do this step. I was actually trying to help a user here, and was using the same procedure which was “default” when ff99SB was the norm, and back then we did not source ions explicitly. Using ff99SB from oldff/leaprc.ff99SB works as (used to be) expected.

I’m thinking that the new way of doing things will confuse the old users, already accustomed to not need to load ions explicitly. Do you think we could add a warning in LEaP, telling them to do so when they try to use “AddIons”? Maybe something like:

> AddIons2 gab NA 0
*** WARNING ***
You have not loaded any ion parameter file. As from version XXX, ion parameter files are not loaded by default, as the best ion parameters are water model dependent. You now need to issue a command like:
loadAmerParams frcmod.ionsXXX

(Please look into the [manual?] for details.)


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Received on Wed Feb 26 2014 - 05:30:05 PST
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