Re: [AMBER] error with ambertools12 and amber10 installation

From: vaibhav dixit <vaibhavadixit.gmail.com>
Date: Wed, 25 Jul 2012 14:54:11 +0530

Dear Prof. Case and amber users,
Thanks for your valuable suggestions and time.
I have tried the changes that you had suggested earlier. The modified
na_anal.nab file is attached for your kind reference. But I'm getting the
following error in the make -f Makefile_at command. Please suggest how I
can get rid of this syntax error.
Also I noticed that there was a problem in compiling g77 during the
./configure_at gcc command (given at the end of this message).
I tried to install g77 but can't figure out which is the best version for
my system (ubuntu 12.01, I have updated using command given at
http://ambermd.org/ubuntu.html)

Syntax error 
----
rm -f cifparse.a
ar rv cifparse.a lex.cif.o cifp.tab.o cifparse.o
ar: creating cifparse.a
a - lex.cif.o
a - cifp.tab.o
a - cifparse.o
ranlib cifparse.a
mv cifparse.a /home/gncp/Documents/GNCP/MD/amber10/lib
make[1]: Leaving directory
`/home/gncp/Documents/GNCP/MD/amber10/src/cifparse'
(cd nab && make install )
make[1]: Entering directory `/home/gncp/Documents/GNCP/MD/amber10/src/nab'
./nab  -c -DDATDIR='"/home/gncp/Documents/GNCP/MD/amber10/dat"'  na_anal.nab
na_anal.nab:1777 syntax error
nab2c failed!
make[1]: *** [na_anal.o] Error 1
make[1]: Leaving directory `/home/gncp/Documents/GNCP/MD/amber10/src/nab'
make: *** [install] Error 2
--------------
g77 error during configure command
------------
gncp.Admin:~/Documents/GNCP/MD/amber10/src$ ./configure_at gcc
Setting AMBERHOME to /home/gncp/Documents/GNCP/MD/amber10
Warning: the X11 libraries are not in the usual location !
    To search for them try the command: locate libXt
    On Fedora Core 5 install an xorg-x11-devel package.
    On RedHat8 install an XFree86-devel package.
    For the moment Amber will be configured not to build XLEaP.
Testing the C compiler:
      gcc  -m32 -o testp testp.c
OK
Obtaining the C++ compiler version:
      g++ -v
The version is ../src/configure
4.6.3
./configure_at: 509: [: -lt: unexpected operator
OK
Testing the g77 compiler:
     g77 -O2 -fno-automatic -finit-local-zero -o testp testp.f
/usr/bin/ld: cannot find crt1.o: No such file or directory
/usr/bin/ld: cannot find crti.o: No such file or directory
/usr/bin/ld: cannot find -lgcc_s
collect2: ld returned 1 exit status
./configure_at: 539: ./configure_at: ./testp: not found
Unable to compile a Fortran program using g77 -O2 -fno-automatic
-finit-local-zero
Testing the gfortran compiler:
     gfortran -O1 -fno-automatic -o testp testp.f
OK
Testing flex:
OK
Configuring netcdf; (may be time-consuming)
NETCDF configure succeeded.
The configuration file, config.h, was successfully created.
The next step is to type 'make -f Makefile_at'
gncp.Admin:~/Documents/GNCP/MD/amber10/src$ ./configure_at gcc
-----------
On Fri, Jul 20, 2012 at 5:59 PM, David A Case <case.biomaps.rutgers.edu>wrote:
> On Fri, Jul 20, 2012, vaibhav dixit wrote:
>
> > I have made the following change in the Makeinstall_at file
> > ----
> > #    nab, leap, and sleap:
> >     (cd cifparse && make install )
> > #    (cd nab && make install )
> >
> >     (cd nss && make install )
> > --------
> > but there is the following error
>
> Well, doing things like hacking makefiles is indeed likely to lead to
> problems.
>
> > make[1]: /home/gncp/Documents/GNCP/MD/amber10/bin/nab: Command not found
>
> As the error message indicates, nss depends on nab, so it doesn't make
> sense
> to skip nab and still try to compile nss.
>
> > Please suggest how I can try to fix this.
>
> I made two suggestions in my earlier email; not sure why you didn't try
> them
> out:
>
> (1)
> > > The fix is here:
> > >    http://archive.ambermd.org/201201/0318.html
> > >
>
> (2)
> > > upgrade to the current codes if at all possible.
>
> ...dac
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
-- 
With regards
Vaibhav A. Dixit
Ph.D. Scholar
Department of Medicinal Chemistry
Natl. Inst. Pharm. Edu. & Res. (NIPER)
Sector 67, Phase X,  S.A.S. Nagar (Mohali)
Punjab -160 062 INDIA
Phone (Mobile): +919915214408
E-mail: vaibhavadixit.gmail.com
www.niper.nic.in

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Received on Wed Jul 25 2012 - 02:30:03 PDT
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