[gmx-users] Problem with Prdrg with NR5

[Anton Feenstra]

Daan van Aalten wrote:
> 
> On Tue, 12 Mar 2002, Anton Feenstra wrote:
> 
> > I think PRODRG only supports united atoms (i.e. implicit hydrogens).
> > IMO that is a missing feature. Nevertheless, in this case it would
> > be trivial to add the missing hydrogen by hand. Alternatively, you
> > might add a Carbon atom in stead of the Hydrogen, feed that to
> > PRODRG, and modify the Carbon back to hydrogen yourself, and also
> > fix the atomtype of the Nitrogen (which probably depends on how many
> > carbons are bound to it).
> 
> That is an incorrect statement - implcicit hydrogens are used only for
> APOLAR hydrogens. All hydrogens in the input drawing are discarded and
> PRODRG uses a set of rules for dtermining which atom show have polar
> hydrogens added. In case of aromatic cyclics containing nitrogens this is
> not a trivial problem and PRODRG does indeed not get it always right.
> 
> Daan

Sorry Daan, you're right. I meant to say that PRODRG does not keep
explicit hydrogens when you put them in the input. But this is a
real problem, for e.g. aromatic compounds one often wants all ring
hydrogens explicit. This is (I think) not supported by PRODRG.

Maybe it wouldn't be too much work to have a choice wheter PRODRG
should manage where to put hydrogens or not, or wheter that should
be determined (partially?) by the input...

Nevertheless, I think I should stress the fact that I find PRODRG
a good piece of work and defenitely very useful. But, as we also see
often for Gromacs, the better useful a program is, the more people
will want to use it for other purposes... ;-) Let's just say that
there is always room for improvement!

-- 
Groetjes,

Anton
 ________ ___________________________________________________________
|        | Anton Feenstra                                            |
| .      | Dept. of Pharmacochemistry - Free University Amsterdam    |
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