[gmx-users] charges in .gro

[Daan van Aalten]

Hi Erik/David

Obviously ab initio QM methods are far superior to anything PRODRG (or
indeed any "3-second" program) can ever do - and I don't want to contend
that!

My issue was more with people claiming something doesn't work
without providing any evidence. For instance, last week someone claimed
PRODRG produces puckered phenyl rings, but when asked for their input
coordinates the reply was nothing but silence.

We are committed to providing this program/server to help others do their
projects - we can only improve it if we get constructive feedback.

cheers

Daan

On Thu, 8 Dec 2005, Erik Lindahl wrote:

> Hi Daan,
>
>
> On Dec 8, 2005, at 9:23 PM, Daan van Aalten wrote:
>
> >
> > Hi Rama
> >
> > I would be grateful if you could back up that "not reliable" statement
> > with some actual examples.
>
> This is certainly not an argument in the current discussion, but
> reading it I remembered that I had problems with a carbonate ion in
> Lactoferrin a while ago. This are the lines:
>
> ATOM   5317  C   CO3   695     -29.141  24.537   0.765  1.00
> 29.28      1LCF5590
> ATOM   5318  O1  CO3   695     -27.891  24.233   0.580  1.00
> 30.58      1LCF5591
> ATOM   5319  O2  CO3   695     -29.845  23.937   1.726  1.00
> 34.74      1LCF5592
> ATOM   5320  O3  CO3   695     -29.904  25.364   0.095  1.00
> 26.35      1LCF5593
>
> If I recall correctly I ended up with neutral charge by default, and
> charge -1 (instead of -2) when using full charges.
>
> Now, I _do_ know I should just have used a proper carbonate ion in
> the G96 FF, but I was a bit lazy and just submitted all
> heterocompounds...
>
>
> As for the "reliability": you can no doubt get pretty good charges
> from QM if you start with proper Lewis electron diagrams, minimize
> all possible conformations, spend a week doing gaussian calculations,
> ponder whether you should use implicit QM solvation potentials,
> extract potentials on a dense grid, and finally do two-step RESP-
> fitting. This far I've spent >3 year of CPU time just for DPPC
> headgroup QM runs, and we have just begun fitting the torsion
> potentials.  On the other hand, ProDRG provides a very good
> approximation for most molecules in ~3 seconds.
>
> Life is all about choices!
>
> Cheers,
>
> Erik
>
>
>
> -----------------------------------------------------------
> Erik Lindahl  <lindahl at sbc.su.se>
> Assistant Professor, Stockholm Bioinformatics Center
> Stockholm University, SE 106 91 Stockholm
> Phone: +46 8 5537 8564     Fax: +46 8 5537 8214
>
>
>
>
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##############################################################################
Dr. Daan van Aalten                    Wellcome Trust Senior Fellow / Reader
Wellcome Trust Biocentre, Dow Street   TEL: ++ 44 1382 344979
Div. of Biol.Chem. & Mol.Microbiology  FAX: ++ 44 1382 345764
School of Life Sciences                E-mail: see WWW page
Univ. of Dundee, Dundee DD1 5EH, UK    WWW: http://davapc1.bioch.dundee.ac.uk