[gmx-developers] Hardcoded (bad) parameters in dummy code...
lindahl at stanford.edu
Sun Jun 9 21:23:39 CEST 2002
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.
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