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
