[AMBER-Developers] Ions parameters in ff12SB

From: Gustavo Seabra <gustavo.seabra.gmail.com>
Date: Wed, 26 Feb 2014 10:06:01 -0300

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?
  2. Isn’t it going to break old LEaP scripts that use “Na+” explicitly?

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
26 NA ions required to neutralize.
Using default radius 1.50 for ion NA
Adding 26 counter ions to "gab" using 1A grid
Grid extends from solute vdw + 1.50 to 7.50
Resolution: 1.00 Angstrom.
grid build: 0 sec
Calculating grid charges
charges: 26 sec
Placed NA in gab at (-11.24, 14.22, -10.10).
Placed NA in gab at (-11.24, 37.22, -15.10).
[…]

Done adding ions.

> solvatebox gab TIP3PBOX 10
 (using default radius 1.500000 for NA)
 […]
  Total vdw box size: 82.140 113.978 101.616 angstroms.
  Volume: 951337.446 A^3
  Mass > 485323.358 amu, Density > 0.847 g/cc
      (type - hence mass - of one or more atoms could not be found)
  Added 23751 residues.

> saveamberparm gab gab.prmtop gab.inpcrd
Checking Unit.
Building topology.
Building atom parameters.
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+
[…]
Parameter file was not saved.




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Received on Wed Feb 26 2014 - 05:30:03 PST
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