I believe you downloaded it and installed it in the wrong place maybe ?
Your output shows "/usr/local/amber9/exe/" and you untarred/unzipped
ambertools 1.5 in /Download/
On 5/7/11 6:01 AM, souvik sur wrote:
>
> Dear sir,
> Thank you for your kind concern,I was trying with the following commands for running antechamber in my system,after
> downloading AmberTools-1.5:
>
> $ tar jxvf ~/Download/AmberTools-1.5.tar.bz2 -C /opt$ ./configure -macAccelerate gn
> $ make
> $ cd ../test
> $ cd ../src
>
> $ make clean
>
> after the command "clean" there showed no error and also it was passed the "test" command showing no error.After doing all the things, then I tried to run "sustiva" for antechamber but then it showed:
>
> [root.localhost ~/souvik]# $AMBERHOME/exe/antechamber -i sustiva.pdb -fi pdb -o sustiva.prepin -fo prepi -c bcc -s 2
> Running: /usr/local/amber9/exe/bondtype -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac -j full
>
>
> Running: /usr/local/amber9/exe/atomtype -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff
>
> Total number of electrons: 160; net charge: 0
>
> Running: $AMBERHOME/exe/divcon
> forrtl: severe (174): SIGSEGV, segmentation fault occurred
> Image PC Routine Line Source
> divcon 08336186 Unknown Unknown Unknown
> divcon 081F4BE0 Unknown Unknown Unknown
> divcon 081BE548 Unknown Unknown Unknown
> Error: cannot run "$AMBERHOME/exe/divcon" of bcc() in charge.c properly, exit
>
> Can I able to understand my problem now?
>
>
> regards,
> Souvik Sur
> Ph. D. Student
> Department Of Chemistry
> University Of Delhi
> India
>
>
>
>
>> Date: Fri, 6 May 2011 10:02:01 -0400
>> From: case.biomaps.rutgers.edu
>> To: amber.ambermd.org
>> Subject: Re: [AMBER] Antechamber loading Problem
>>
>> On Fri, May 06, 2011, souvik sur wrote:
>>>
>>> Unknown UnknownError: cannot run "$AMBERHOME/exe/divcon"
>>
>> As you already know, you need to upgrade.
>>
>>> already untarred the AmberTools 1.5 tar file and also compiled
>>> openmpi-1.4 tar file which is
>>> needed for installation.
>>
>> First, openmpi (or any MPI) has nothing to do with antechamber. Second,
>> you don't tell us what you did after untarring the AmberTools 1.5 file, how
>> you configured and compiled it, or what the problem is with the new code.
>> You also don't say (in any of these messages) anything about the results of
>> running the test suite. I can guess(!?!) that you came across sustiva in the
>> test suite, but this is only a guess, and there is no information given about
>> the results of any other tests.
>>
>> So, please put just one question in each email, and *carefully* describe
>> exactly what you did, and exactly what the result was. Don't do anything with
>> parallel options until you understand how the serial codes work.
>>
>> ....dac
>>
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Dr. Adrian E. Roitberg
Associate Professor
Quantum Theory Project, Department of Chemistry
University of Florida
on Sabbatical in Barcelona until August 2011.
Email roitberg.ufl.edu
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Received on Sat May 07 2011 - 01:00:02 PDT
