[gmx-users] Reordering of water molecules with Na+ ions coordinates in xtc message

chris.neale at utoronto.ca chris.neale at utoronto.ca
Sun Jan 2 18:04:54 CET 2011

Dear Leila,

Please address my previous question. *Are you using the correct  
Makefile.template?* Did you do the compilation of gromacs? If not, I  
suggest that you compile gromacs again (and not into /usr/ but into  
./exec or some such local dir) and use your files from there.

If you still can't get the file to work in this way, then just  
download a fresh version of gromacs4.0.7, name it with a special  
directory, make the modification directly to the *original* trjconv,  
and compile it. Now you will have a special version of trjconv.

I can't help you any more because the steps that I suggested worked  
for me. It is unclear exactly what you are doing wrong, but I suspect  
that it is simply that you are not actually following the steps that I  
laid out.


-- original message --

I did all of steps again. this tims when compile Makefile.my_tool by both of
make and gmake:

make: *** No rule to make target `my_tool.o', needed by `my_tool'.  Stop.

my Makefile.my_tool is as follows:

# Generated automatically from Makefile.in by configure.
# This is a Gromacs 3.0 my_tool makefile for your own utility programs.
# Copy this file to whatever directory you are using for your own
# software and add more targets like the my_tool one below.
# If you are using gmake it is relatively straightforward to add
# an include based on environment variables (like previous Gromacs versions)
# to select compiler flags and stuff automatically, but below it is static:

# Variables set by the configuration script:
LIBS         = -lmd -lgmx -lxml2  -L/usr/lib64 -lnsl -lfftw3f -lm   -lSM
-lICE -lX11
LDFLAGS      = -L/usr/local/gromacs/lib
CFLAGS         = -O3 -fomit-frame-pointer -finline-functions -Wall
-Wno-unused -funroll-all-loops   -I/usr/include/libxml2
-I/usr/local/gromacs/include -I/usr/local/gromacs/include/gromacs
CC           = cc
LD           = $(CC)

# The real make targets - note that most make programs support
# the shortcut $^ instead of listing all object files a second
# time, but we cannot count on it...

my_tool:    my_tool.o
         $(LD) $(LDFLAGS) -o $@ my_tool.o $(LIBS)
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