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
>
>
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Received on Fri May 06 2011 - 21:30:03 PDT
