Dear Sir,
When I use (./rism1d) command in terminal then it shows ‘input file not specified’, but when I used (./rism3d or ./rism3d.snglpnt or sander.RISM as given in the Amber11 users’ manual at page 62) all of it shows ‘no such file or directory’. In exe folder 75 executable files are present (such as sander, tleap, rism1d, nab etc), but there is no executable file having name (rism3d or sander.RISM or rism3d.snglpnt). So it seems that rism3d.snglpnt is not build during Amber tools installation.
You and Dan suggested that to built rism3d.snglpnt recompilation of Amber Tools is necessary. Is the recompilation same process like Amber tools installation given in Amber tools users’ manual from page 13 to 14? Before recompiling the Amber tools I need your suggestion. As in my existing system already Amber tools are compiled, so during recompilation is it necessary to delete or remove the previous file? If no, then I want to do the following step-
Create a directory under usr/local (say usr/local/software).
(By the way, previously Amber tools was installed in usr/local directory.)
Keep two zip files in software folder (Amber11.tar.bz2 and AmberTools-1.4.tar.bz2).
Extract the files in usr/local/software directory as-
cd /usr/local/software
tar xvfj AmberTools-1.4.tar.bz2
I think this will produce ‘amber11’ in this directory. Then-
export AMBERHOME=/usr/local/software/amber11
cd amber11/AmberTools/src
(the directory is now usr/local/software/amber11/AmberTools/src)
./configure gnu
make
cd ../test
make test
Is the rism3d.snglpnt build at this step? Can I see any error messages after this step if rism3d.snglpnt is not build?
In manual after this step preparation of parallel (MPI) version are given. Can I avoid this step? If I avoid this step then is it possible to run the 3D-RISM. In first time installation this step (preparation of parallel version) was avoided.
In the other hand can I carried out recompilation of Amber tools by the following way (without remove the existing files)–
export AMBERHOME=/usr/local /amber11
cd amber11/AmberTools/src
(the directory is now usr/local /amber11/AmberTools/src)
./configure gnu
make
cd ../test
make test
Please let me know.
With the best regards,
Sudarshan.
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Received on Tue Jan 10 2012 - 22:30:03 PST
