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

[Erik Lindahl]

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).

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.

For the normal dummies we should use a database with entries containing 
the type of dummy and parameters for different heavy atoms.
 I'm not sure what to do with the aromatic stuff - unless it can be 
solved trivially I will disable dummy aromatics for now.

Erik