[AMBER-Developers] Chamber support patch for PMEMD

From: Ross Walker <ross.rosswalker.co.uk>
Date: Thu, 15 Oct 2009 13:57:34 -0700

Hi All,

I have made a patch - in the form of a bugfix that patches pmemd to support
Chamber prmtops ready for AmberTools 1.3. My intention is to make this part
of the regular bugfixes. That way we do not have to worry about this patch
and the bug fixes ending up out of sync with each other. Additionally we can
just tell people in the manual to make sure they have applied all the latest
bugfixes. (I will have some additional changes to the manual for ptraj MPI
and updated chamber stuff very soon).

I will update the manual shortly. For the moment I attach the patch file and
would appreciate some people testing it. This patch is pretty complicated
since it patches a LOT of files and creates new files and directories.

It also fixes a number of other minor bugs in pmemd that have recently been
fixed in amber11 cvs.

You can apply this with (assuming you have applied the latest bugfix.all

cp bugfix.26 $AMBERHOME/
patch -p0 <bugfix.26
cd $AMBERHOME/src/pmemd/
make clean
make install

cd $AMBERHOME/test/
export DO_PARALLEL='blah blah blah'
make test.pmemd

One problem I have come across that I am hoping someone here has a
suggestion for how to solve.

On my machine this patch creates the chamber tests in $AMBERHOME/test and
this include 4 Run.xxx files in $AMBERHOME/test/chamber/md_engine/dhfr and

The issue is that these get created with 600 permissions so when make
test.pmemd runs it reports that permission is denied for these 4 Run files.
Chmod 700 fixes this. Any idea how we can address this without having to
change the instructions we have for applying patches etc?

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 Thu Oct 15 2009 - 14:00:04 PDT
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