Re: compiling NAMD failed on windows with Cygwin

From: Axel Kohlmeyer (
Date: Mon Dec 29 2008 - 09:36:45 CST

On Mon, 29 Dec 2008, accomp lin wrote:

J> Dear developer of NAMD:

dear jiaqi,

J> I'm compiling NAMD on windows with Cygwin. I tried several time but failed. The problem is that i didn't set the directory of charm5.9, tcl, fftwin .arch file correctly. Aftermaking this right, I finally got the NAMD compling on progress. But I then I got the follows error:
J> -LE:\Mr.Lin\comp\NAMD_2.6_Source\tcl/lib -ltcl8.3 \
J> -LE:\Mr.Lin\comp\NAMD_2.6_Source\fftw/lib -lsrfftw -lsfftw \
J> obj/dcdplugin.o \
J> \
J> -lm -o namd2
J> E:Mr.LincomNAMD_2.6_Sourcecharm-5.9/net-Cygwin/bin/charmc: not found
J> make: *** [namd2] Error 127

J> I browsed to the .../net-Cygwin/bin/ directory but I found a charmc
J> link is actually there. So what's my problem? Is that becasue some
J> "\" is lacked in the command? Where can I find the command so I can
J> add the "\" to it myself?
J> Please help

please read the cygwin documentation more carefully!
cygwin emulates a unix environment, so everything you
provide - for example path names - has to be giving
in "unix"-format and the unix path separator is the
forward slash '/'. the backward slash '\' is an escape
character in scripts and makefiles and as such indicates
to use the next character literally. because of that
your build script cannot find the charmc script, because
it is looking in the wrong location.

to produce a backslash you'd have to use '\\' (or '\\\\'
in case the string is interpreted twice), but i recommend
to specify all paths with '/' to avoid this.


J> Thank you!
J> Jiaqi


Axel Kohlmeyer
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
If you make something idiot-proof, the universe creates a better idiot.

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