[gmx-developers] Hardcoded (bad) parameters in dummy code...

Anton Feenstra feenstra at chem.vu.nl
Mon Jun 10 13:13:45 CEST 2002

Erik Lindahl wrote:
> Hi,
> When trying to use dummies with OPLS I discovered that the
> dummy-generating code in pdb2gmx is seriously broken. All parameters are
> *hardcoded* for the Gromacs (not even Gromos96 - there are a couple of
> different paramters) forcefield without a single warning to tell the
> user this is the case. In several places, the dummy code also makes
> assumptions about atom type names (hardcoded here too...), and it looks
> as if the position of dummy hydrogens might determined by the
> coordinates generated in pdb2gmx and not the forcefield values. (It
> isn't easy to tell, since there are very few comments).

Yes - This was mostly written before the Gromos96 ff was implemented
and after comparison with the gromacs forcefields, I felt that the 
differences were negligible. However, you are right that a comment
at least somewhere would have been appropriate - I appologize...

But, if I remember correctly, for '-dummy hydrogens', *all* parameters
are calculated from forcefield parameters. Only for the 'aromatics'
all parameters and atom names are hard-coded; if you try to work
that out starting from the bare aromatic sidechain topology and
assorted parameters, thing *really* get complicated... ;-(

The atom type is only checked for "NL", which is the type for
an umbrella-shaped -NH2 group, but nothing in the dummy code should 
depend on the input coordinates, only on some of the forcefield 

> In the current state it's essentially hopeless trying to fix this code,
> so unless somebody else volunteers I'm about to toss it completely and
> replace it with a much less automated version that at least doesn't try
> to hardcode stuff.

Hmm. This is not making me happy. And that on the day I got my
thesis printed... :(

> For the normal dummies we should use a database with entries containing
> the type of dummy and parameters for different heavy atoms.

Sounds good.

>  I'm not sure what to do with the aromatic stuff - unless it can be
> solved trivially I will disable dummy aromatics for now.

Must you be so drastic? It works the way it is, it is consistent at 
least with ffgmx and ffgmx2, and the differences with ffG43a are
realy very minimal (if at all, I haven't re-checked). We should
however ofcourse issue a clear warning about which parameters are
used. Wouldn't that be a good alternative to tossing?


 ________ ___________________________________________________________
|        | Anton Feenstra                                            |
| .      | Dept. of Pharmacochemistry - Free University Amsterdam    |
| |----  | De Boelelaan 1083 - 1081 HV Amsterdam - The Netherlands   |
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| ' __   | Feenstra at chem.vu.nl - http://www.chem.vu.nl/afdelingen/FAR|
|  /  \  |-----------------------------------------------------------|
| (    ) | Dept. of Biophysical Chemistry - University of Groningen  |
|  \__/  | Nijenborgh 4 - 9747 AG Groningen - The Netherlands        |
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|  /  \  | K.A.Feenstra at chem.rug.nl - http://md.chem.rug.nl/~anton   |
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|  \__/  | "Confirmed" (Star Trek)                                   |

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