possible problem with Sire.IO.Amber.readCrdTop()

[hannes....@gmail.com]

Hi,

I just ran into a problem with the parmtop reader.

I am trying to get the 1,4 pairs from the intrascale property and check for both Sire.MM.CLJScaleFactor.lj() and .coulomb() to be zero. Occasionally I get double counting (but indices swapped). Work-around on my side is obvious but is this expected behaviour?

Many thanks,
Hannes.

(Just remembered that this group exists :-)

[hannes....@gmail.com]

Oh and the vdW sigmas appear to be multiplied by about 1.7818 but I can't make out where this "magical" conversion factor comes from.

[Christopher Woods]

  Hi Hannes,

Sorry for not replying sooner - had a migraine for most of this evening.

I don't know about the 14 scale factors. I've taken a quick look at the amber topology reader and it is all set in 

static void setNonBondedPairs(MolEditor &editmol, int pointer,

Is this setting the values that you expect? (Have you used qDebug to print was is set and wht you read for a small molecule?)

The LJParameter object stores the square root of the sigma and epsilon values (sigma in angstroms). I don't recall any factor of 1.78. Where exactly do you see this value? (short example code or function that you are calling)

   Cheers,

   Christopher

Sorry for abruptness. Sent from my iPad

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[hannes....@gmail.com]

Many thanks, Chris.

This factor confused me because Gromacs for example wants sigma while the original AMBER force field files store _rstar_.  That's all the "magic" that is to it.

I will have another look into setNonBondedPairs() and see what is going on.  I'll come back if there are further questions.

Cheers,
Hannes.