Bug #434

pdb2gmx opens all rtp files

Added by David van der Spoel over 10 years ago. Updated over 10 years ago.

Erik Lindahl
Target version:
Affected version - extra info:
Affected version:


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.


#1 Updated by Berk Hess over 10 years ago

I intended pdb2gmx to open all rtp files.
This can be useful if you want to add and rtp entry of some molecule
to an existing force field.

But if this leads more often to unwanted than to wanted behavior,
we can turn this feature off.


#2 Updated by Erik Lindahl over 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.

#3 Updated by David van der Spoel over 10 years ago

I could live with pdb2gmx open additional files in the force field directory, and being able to read multiple files makes it easier to add new building blocks rather than messing up the "official" files.

#4 Updated by Erik Lindahl over 10 years ago

Being able to read multiple files - if asked to - is a nice feature (although doing it with includes might be cleaner). However, always opening all files in the current directory just based on the extension, without any chance to prevent it, is not ;-)

#5 Updated by Berk Hess over 10 years ago

I added a option -cwd top pdb2gmx, default off.

Note that there was already the -rtpo option and by default
pdb2gmx would not allow multiple rtp defintions of the same name
in different files.


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