On Apr 28, 2011, at 5:47 PM, "B. Lachele Foley" <lfoley.uga.edu> wrote:
> In order to do a proper test of tleap versus sleap, we did the following:
>
> 1. Hacked 1-4 scaling writes into tleap.
> 2. Wrote a separate program, independently, that adds SCEE/SCNB to an existing top.
>
> Then, we compared output from post-processing an existing trajectory for a system containing both a glycan and a protein using top files produced by:
>
> 1. old tleap plain -vs- new tleap with SCEE/SCNB written out, but manually changed back to AMBER defaults.
By this, I assume you mean hack the prmtops to have 1.2 for all scee and 2.0 for all scnb? (or 1 over that as it were)
> 2. new tleap with SCEE/SCNB -vs- the post-processor we wrote
> 3. new tleap with SCEE/SCNB -vs- sleap with SCEE/SCNB
>
> The results from 1 were identical, as
Results are energies from sander?
> were the results from 2. There was a small difference in the sleap dihedrals from 3 (explained below).
>
> If you agree with our procedure and with our assessment of the sleap dihedral issue, we will push the changes to tleap.
Seems reasonable to me. Does it prit out any SCEE or SCNB sections if those sections don't exist in the parm files? What if it only exists in some of the parm files?
>
> We'll also make the post-processor available on our site, but we can add it to Amber, too, if you want. We'll probably post the tleap mods to our site, too, to make sure the carb folks see them.
My personal vote here is to either not post the post-processor to amber or keep it undocumented or something. If you guys made tleap do it, people should just use that. This seems like a strange stance coming from someone pushing a plethora of prmtop utilities, but the more we just create additional programs to avoid hacking leap, the more hopelessly complex it will be for a user to set up a prmtop "correctly". Especially if/when multiple utilities have to be used together in a specific order! My vote is to do whatever possible to include stuff in leap itself, and on top of that maybe create a little utility (GUI and CL?) that unifies the other utilities in a common wrapper to simplify the process of post processing a topology file.
>
> Here's the sleap issue.
>
> Consider these atom types relevant to an improper dihedral: CG, N, H, C
>
> And these two impropers:
> parm99 X -X -N -H 1.0 180. 2. JCC,7,(1986),230
> Glycam06 X -X -N -CG 1.5 180. 2. X -X -N -H
Aye... What would we even say is the right approach here?
>
All the best,
Jason
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Thu Apr 28 2011 - 19:00:02 PDT
