Re: [AMBER-Developers] Chamber support patch for PMEMD

From: Scott Brozell <>
Date: Fri, 16 Oct 2009 03:34:23 -0400


On Thu, Oct 15, 2009 at 01:57:34PM -0700, Ross Walker wrote:
> 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 files in $AMBERHOME/test/chamber/md_engine/dhfr and
> dhfr_cmap
> 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?

On my machine they get created with 644 per my shell rc umask command.
%man patch
       Context diffs cannot reliably represent the creation or deletion of empty
       files, empty directories, or special files such as symbolic links. Nor
       can they represent changes to file metadata like ownership, permissions,
       or whether one file is a hard link to another. If changes like these are
       also required, separate instructions (e.g. a shell script) to accomplish
       them should accompany the patch.


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Received on Fri Oct 16 2009 - 01:00:02 PDT
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