On Wed, Feb 26, 2014, Gustavo Seabra wrote:
>
> 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.)
I suspect you are using an outdated version. As of commit
13c59fcf5974899ff05b (on 22Feb14) the old names for Na+, K+, Cl- are present.
See if doing a "git pull" doesn't help.
> 1. Is this the expected behaviour?
> 2. Isn’t it going to break old LEaP scripts that use “Na+” explicitly?
See above. But we do want to encourage people to use PDB-standard
atom and residue names. Given that there are more than 17,000 components
in the PDB, just making up our own names (the CHARMM approach) is increasingly
awkward, and does not allow us to make use of lots of information about these
components that is available at RCSB.
[As an aside, we're not ready to change the non-standard way we handle
carbohydrates and lipids. But we do need to see if there is some way to
(a) warn users about this; (b) potentially use lower-case (or mixed case)
residue names that won't conflict with the all-upper-case residue names used
by the PDB.]
>
> 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).
> 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 load the appropriate frcmod file for ions? This doesn't look like it
has anything to do with the residue and atom names. I encourage people to put
on their thinking caps about this: how can we best help users with similar
problems? The simplest answer is to provide a better error message--have
tleap identify that it is an ion parameter that is missing, then print out
a better message about the need to load the appropriate ion parameters (or
maybe just a pointer to the Ions section of the Manual).
Or, if there are missing ions, figure out what water model is active (How???)
and automagically load the correct parameters. This would be too big a change
for Amber14, I think.
...dac
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Received on Wed Feb 26 2014 - 06:00:04 PST
