pdb2gmx opens all rtp files
If I run pdb2gmx in a directory where there happens to be a randomly named rtp file, this is opened instead of the one I select. E.g. I select the encadv force field and pdb2gmx finds a file koko.rtp in my directory and uses that instead of the encadv file. pdb2gmx then bails out because of a mismatch between the encadv atomtypes.atp file and my koko.rtp file. This is confusing for the user, but could also lead to unnoticed problems, e.g. if you select the gromos force field for water, but happen to have the cyclohexane force field file in your directory.
#2 Updated by Erik Lindahl almost 10 years ago
In general, we should never try to do "smart" stuff that the user hasn't told us. This has already led to tons of problems (hydrogens and patches) in pdb2gmx, and it's recipe for disaster, IMHO.
Either we stick to the default force field name, or we provide a flag to specify which files to open. Then, if it's convenient, we can of course consider allowing a wildcard in the specification.