VMD-L Mailing List

From: fvlieffe (Francois.Van.Liefferinge_at_ulb.ac.be)
Date: Tue Jul 14 2015 - 07:13:10 CDT

hi all,

background: I'm trying to parametrize the thiamine pyrophosphate by the
method divide-and-conquer.
I divide my molecule in 3 parts: the 4-amino-pyrimidine (6-ring), the
thiazolium (5-ring with a positively
charged N) and the pyrophosphate.
I already have parameters for the pyrophosphate and I'm working and the
2 former parts.

Firstly, for the pyrimidine and the thiazolium, I reach the water
interaction step in fftk, the step in itself is not difficult to realize
but after uploading the psf and pdb, come the moment to assign donor or
acceptor to the different atoms.
If I use the autoDetect indices button on fftk, for both (pyrimidine and
thiazolium): every atoms are "acceptor".

It's a bit hard to believe because both contains aliphatic Hydrogen,
wich are common donor. So I do not know if I made a mistake somewhere
or fftk has some issues with that.

Secondly, I went a little further, generating the gaussian input "donor"
AND "acceptor" for all the pyrimidine and the thiazolium.
After running the gaussian calculation for both molecules (donor and
acceptor), the results I obtained for the pyrimidine confirm my believes
(atoms I expected to be donor and acceptor)
But in the case of the thiazolium it was more problematic: all the atoms
were donors. For example in the thiazolium ring there is a sulfur
atom, this sulfur atom with the gaussian input "acceptor" has a distance
of 31 angtrom with the water molecule when the equilibrium is reached.
but this sulfur atom with the gaussian input "donor" has a distance of
3.28 angstrom with the water molecule.

So my question is: when I work with a positively charged molecule
(charge on the N of the 5 membered ring) does all the atoms of the
ring become
"donor" for the water interaction step?

because for my thiazolium it appears to be so.

thank you

regards 

-- 
Van Liefferinge François
Phd Student in Chemistry
S.F.M.B., Université Libre de Bruxelles
Campus Plaine CP 206/2
Bâtiment BC, local 1C4.107
Blvd. du Triomphe
B-1050 Bruxelles
BELGIQUE