VMD-L Mailing List

From: Evandro Semighini (epsemighini_at_gmail.com)
Date: Tue Jul 14 2015 - 07:30:44 CDT

Hello,

The issue with "only acceptor" happened to me when I used as input a PDB
file without the connection table.
Check if your gaussian input files atom names are correct, or if all of
them are named as dummy atoms "x".
If it does, create a pdb file with the connection table, Qimera and
Avogadro used to work fine for me.

I guess this explains the 31 Angstom distance of the seccond question.

Just my 1 cent. ;)

Best regards,

Evandro

2015-07-14 9:13 GMT-03:00 fvlieffe <Francois.Van.Liefferinge_at_ulb.ac.be>:

> 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
>
>