Hi Dave,
On Feb 26, 2014, at 10:57 AM, David A Case <case.biomaps.rutgers.edu> wrote:
> 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 I suspect you are using an outdated version.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.
As far as I can tell, I’m using an up-to-date version. After Jason’s changes, I did a “git clean -d” as you suggested, followed by “git pull”. Now,
$ git status
On branch master
Your branch is up-to-date with 'origin/master'.
nothing to commit (use -u to show untracked files)
>> 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
No, I was not loading the frcmod file. I was trying to follow what used to be default “back in the 99SB days” :)
Gustavo.
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Received on Wed Feb 26 2014 - 06:30:03 PST
