Re: [AMBER] amber10 installation problem

From: Lan JIN <>
Date: Fri, 10 Jul 2009 08:41:34 +0100

Well, I did 'make clean' instead of 'make -f Makefile_at clean'.

This time I do 'make -f Makefile_at clean' and 'make -f clean' so that I can recompile both of them. Both AmberTool and Amber10 pass the installation unless there are some ignored error for AmberTool. Do I need to consider these ignored errors providing the installation is done? 

The following are the possible failure test result, all others PASSED. The TEST_FAILURES.diff is attached as well. Will they cause any problem especially for the 'lmod optimization energy difference' and the last one (Where can I find this impose.out.dif file? It seems there is no 'polymer' directory to go into.) ?

Running test of randomized embedding

< radius of gyration:    7.340
> radius of gyration:    7.249
   FAILED (OK if gyration radius is about 7 or 8)

Running test to do simple lmod optimization

< Glob. min. E         =     -122.793 kcal/mol
> Glob. min. E         =     -129.345 kcal/mol
   FAILED (probably OK if energy is -115 to -125)

cd antechamber/tp && ./
diffing with tp.mol2
possible FAILURE:  check tp.mol2.dif
cd polymer; ./Run.impose
rm: cannot remove‘impose.out’: no such file or directory
rm: cannot remove‘impose.mol2’: no such file or directory
diffing with impose.out
possible FAILURE:  check impose.out.dif

I found that if I did 'make -f Makefile_at test' before compiling AMBER10, the test process stopped with an error as follows (all previous are PASSED). After compilation of AMBER10 and did the test, the error just disappeared. I do not know why. Where is this '' file and what is it for?

       comparing sander energies
/usr/local/AMBER/amber10/exe/sander: error while loading shared libraries: cannot open shared object file: No such file or directory
./Run.tleap:  Program error in sander (could be leap input problem)
make: *** [test.leap] error 1


--- 09年7月9日,周四, case <> 写道:

发件人: case <>
主题: Re: [AMBER] amber10 installation problem
收件人: "AMBER Mailing List" <>
日期: 2009年7月9日,周四,下午8:38

On Thu, Jul 09, 2009, Lan JIN wrote:
> I did the following test without editing the config.h file but got error
> messages as well. Does it matter with the mopac6 or something else?

This is weird.  Did you do a "make -f Makefile_at clean" before recompiling?
Does your g77 code work for other programs?  Can you go to the mopac
directory, do "make clean", "make install" and post the entire error log --
usually it is the *first* error, not the last little bit, that gives the most


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Received on Fri Jul 10 2009 - 01:09:24 PDT
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