Yes, I realized that. Actually, deleted the folder and repeated the whole
procedure, and this is working quite well, at least configure, and make end
without any errors.
Thanks,
Majid
________________________________
From: Jason Swails <jason.swails.gmail.com>
To: AMBER Mailing List <amber.ambermd.org>
Sent: Sun, April 10, 2011 2:43:06 PM
Subject: Re: [AMBER] Error in installing Amber Tools
Separately:
http://ambermd.org/bugfixes.html
On Sun, Apr 10, 2011 at 2:18 PM, majid hasan <pu_majidhasan.yahoo.com>wrote:
> Yes, I am going to delete the current folder, and try again. Are these bug
> fixes
> included in 1.4, or do I have to download them separately?
>
> Thanks,
> Majid
>
>
>
>
> ________________________________
> From: Jason Swails <jason.swails.gmail.com>
> To: AMBER Mailing List <amber.ambermd.org>
> Sent: Sun, April 10, 2011 1:59:35 PM
> Subject: Re: [AMBER] Error in installing Amber Tools
>
> I don't know why you're having issues building on Ubuntu -- I do it all the
> time. Make sure you're building AmberTools 1.4. I would suggest
> downloading the latest version and extracting/building it from scratch.
>
> Make sure you apply all of the bug fixes.
>
> On Sun, Apr 10, 2011 at 1:50 PM, majid hasan <pu_majidhasan.yahoo.com
> >wrote:
>
> > Oh sorry, its also the same, 4.4.3
> >
> > Majid
> >
> >
> >
> > ________________________________
> > From: Jason Swails <jason.swails.gmail.com>
> > To: AMBER Mailing List <amber.ambermd.org>
> > Sent: Sun, April 10, 2011 1:49:23 PM
> > Subject: Re: [AMBER] Error in installing Amber Tools
> >
> > What about gfortran?
> >
> > On Sun, Apr 10, 2011 at 1:41 PM, majid hasan <pu_majidhasan.yahoo.com
> > >wrote:
> >
> > > cpp: (Ubuntu 4.4.3-4ubuntu5) 4.4.3,
> > > and same for g++, and gcc. I installed them from ubuntu software
> center.
> > >
> > > I have also attached the complete config.log file. Any ideas?
> > >
> > > Thanks for your help,
> > > Majid
> > >
> > >
> > >
> > >
> > > ________________________________
> > > From: Jason Swails <jason.swails.gmail.com>
> > > To: AMBER Mailing List <amber.ambermd.org>
> > > Sent: Sun, April 10, 2011 12:55:53 PM
> > > Subject: Re: [AMBER] Error in installing Amber Tools
> > >
> > > The configure.log says that cpp sanity check didn't work.
> > >
> > > It's impossible to tell what's going wrong based on the information we
> > > have. Make sure you follow the installation instructions found in the
> > > manual as closely as possible. Also note that there may be permission
> > > issues with installing in /usr/local (see previous posts on the list).
> > >
> > > What version is your cpp, gcc, g++, and gfortran? You can find this
> with
> > > the --version flag for each one.
> > >
> > > On Sun, Apr 10, 2011 at 12:40 PM, majid hasan <pu_majidhasan.yahoo.com
> > > >wrote:
> > >
> > > > Dear All,
> > > >
> > > > I am getting following error when I run make (more output attached)
> > > >
> > > > " gunzip -c -d ../reduce_wwPDB_het_dict.txt.gz >
> > > > /home/majid/down/amber11/dat/reduce_wwPDB_het_dict.txt
> > > > /bin/sh: cannot create
> > > > /home/majid/down/amber11/dat/reduce_wwPDB_het_dict.txt:
> > > > Directory nonexistent
> > > > make[2]: *** [install] Error 2
> > > > make[2]: Leaving directory
> > > > `/home/majid/down/amber11/AmberTools/src/reduce/reduce_src'
> > > > make[1]: *** [install] Error 2
> > > > make[1]: Leaving directory `/home/majid/down/amber11/AmberTools/src/
> '
> > > > make: *** [serial] Error 2
> > > > ubuntu:~/down/amber11/AmberTools/src> "
> > > >
> > > > ./configure gnu went well except this error:
> > > >
> > > > Configuring NetCDF; (may be time consuming)
> > > > NetCDF configure returned 1
> > > > NetCDF configure failed! Ceck the netcdf_config.log file. Continuing
> > but
> > > > NetCDF
> > > > will be skipped.
> > > >
> > > >
> > > > netcdf_config.log file is attached.
> > > > _______________________________________________
> > > > AMBER mailing list
> > > > AMBER.ambermd.org
> > > > http://lists.ambermd.org/mailman/listinfo/amber
> > > >
> > > >
> > >
> > >
> > > --
> > > Jason M. Swails
> > > Quantum Theory Project,
> > > University of Florida
> > > Ph.D. Candidate
> > > 352-392-4032
> > > _______________________________________________
> > > 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
> > >
> > >
> >
> >
> > --
> > Jason M. Swails
> > Quantum Theory Project,
> > University of Florida
> > Ph.D. Candidate
> > 352-392-4032
> > _______________________________________________
> > 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
> >
>
>
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
> _______________________________________________
> 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
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
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http://lists.ambermd.org/mailman/listinfo/amber
Received on Sun Apr 10 2011 - 15:30:01 PDT
