Re: [AMBER-Developers] Comments on patch file for PMEMD 10 Chamber

From: Jason Swails <>
Date: Wed, 7 Oct 2009 22:22:04 -0400

If given rope to hang oneself, someone almost surely will. If determining
whether or not a patch has been applied is as easy as testing the existence
of a file, then I think we should hold the users' hands here. It'll be
sufficiently easy for someone to find the rope to hang themselves with if
they are so inclined (I can't imagine it would be hard to trick a makefile
that a file exists), so everyone leaves happy. Those that want to hang
themselves can, and those that are just feeling their way through the
process get to jump over it. You could also make it plenty verbose, telling
the user what's happening and why, etc. etc.
What does everyone else think?

On Wed, Oct 7, 2009 at 9:51 PM, Ross Walker <> wrote:

> Dear all,
> I just wanted to run an idea past you all for comment.
> AmberTools 1.3 will include the program Chamber which converts a charmm psf
> to a special CHARMM format prmtop file. This can then be used to run charmm
> force field simulations within sander and pmemd. This requires an updated
> version of sander or pmemd which supports such simulations. This exists in
> the AMBER 11 tree but is obviously not present in the released AMBER 10.
> The
> issue at present is that the nature of the changes is that an old version
> of
> sander or pmemd will read the CHARMM prmtop file and simply run giving the
> WRONG answers. This is without any kind of warning.
> An unpatched sander v10 will, fortunately quit with an error. An unpatched
> PMEMD 10 will not, however. Bugfix.22 addresses this and will ensure PMEMD
> 10 quits with an error if fed a CHARMM prmtop. However, this is of course
> the possibility that someone has not patched their code or are using AMBER
> 9
> or earlier.
> With the CHAMBER in AMBERTools 1.3 will be a patch file to update PMEMD 10
> to support these prmtop files. This will have to be applied in order for
> people to be able to use CHARMM prmtops.
> The issue at hand is how much we should hold the users hand here. One
> option
> Mark and I have considered is modifying the AMBERTools 1.3 Makefile to
> check
> if the file charm.fpp exists in $AMBERHOME/src/pmemd/src. This would
> indicate if PMEMD had been updated to support CHARMM prmtop files. If this
> file was not found, which would imply no patching, an old AMBER version or
> no AMBER at all then it will skip compilation of Chamber during the
> AMBERTools build.
> Do people think this is a good idea? Or should we just allow the user
> sufficient rope to hang themselves if they want to and always compile
> Chamber and assume people will have a bugfixed sander / pmemd (which will
> quit if v10) or they have successfully applied the patch.
> Comments?
> All the best
> Ross
> /\
> \/
> |\oss Walker
> | Assistant Research Professor |
> | San Diego Supercomputer Center |
> | Tel: +1 858 822 0854 | EMail:- |
> | | PGP Key available on request |
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Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
AMBER-Developers mailing list
Received on Wed Oct 07 2009 - 19:30:02 PDT
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