Re: [AMBER-Developers] force-field naming (redux)

From: Jason Swails <>
Date: Sun, 8 Mar 2015 21:04:46 -0400

> On Mar 8, 2015, at 6:19 PM, Carlos Simmerling <> wrote:
> I'm not sure give g them a leaprc version to quote in their manuscript is
> enough, even if we can decide it. Most readers won't be able to, and even
> though reviewers should be better about it, we do need to make it easy for
> when reviewers do ask the right questions (or users want to cite the right
> things). I think Lachele's suggestion makes sense - our outputs should list
> what force fields were used and maybe give the citation in some standard
> format, or the doi. That has to someone be in the library files and get
> passed from leap to prmtop to sander/pmemd.... Might not be doable this
> release, but it makes sense to me.
> I think we should try to specify which of the various polymer/ molecule
> params are in each leaprc like Ross said. One complication is that there
> is overlap between atom types so you can't load a protein set without
> loading some sort of nucleic set too. Maybe this was Jason's concern. Maybe
> we just use really long labels on the leaprc files so they know what they
> will get from each?

That was my original concern. You could of course say that leaprc.ff14nuc and leaprc.ff14SB both load parm10.dat and their relevant frcmods, but that the first loads the nucleic libs and the second loads the protein libs in addition. If you load them both together, then all you do is read the same parameters twice... no biggie. You get weird behavior if you try to load ff14nuc with ff14SB, though, given the parm10.dat and parm99.dat differences, and the resulting parameters will depend on which you loaded first, without giving reasonable error messages or warnings.

Longer names are better than what we have now, in my opinion, but are harder to remember, increase the likelihood of typos, and are inconvenient for people working interactively (especially in xleap, where cut-and-paste doesn’t work).
All are minor complaints, IMO. On the upside, it will be familiar for most people (just change the name of the leaprc you source). It will also be more descriptive about the non-protein parts of the FF.

All the best,

Jason M. Swails
Rutgers University
Postdoctoral Researcher
AMBER-Developers mailing list
Received on Sun Mar 08 2015 - 18:30:02 PDT
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