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

From: Ross Walker <ross.rosswalker.co.uk>
Date: Wed, 7 Oct 2009 18:51:53 -0700

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.


All the best

|\oss Walker

| Assistant Research Professor |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk |
| http://www.rosswalker.co.uk | PGP Key available on request |

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Received on Wed Oct 07 2009 - 19:00:02 PDT
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