Dear Francois,
my gfortran output is
Using built-in specs.
COLLECT_GCC=gfortran
COLLECT_LTO_WRAPPER=/usr/lib/gcc/i686-linux-gnu/4.6/lto-wrapper
Target: i686-linux-gnu
Configured with: ../src/configure -v --with-pkgversion='Ubuntu/Linaro
4.6.3-1ubuntu5' --with-bugurl=file:///usr/share/doc/gcc-4.6/README.Bugs
--enable-languages=c,c++,fortran,objc,obj-c++ --prefix=/usr
--program-suffix=-4.6 --enable-shared --enable-linker-build-id
--with-system-zlib --libexecdir=/usr/lib --without-included-gettext
--enable-threads=posix --with-gxx-include-dir=/usr/include/c++/4.6
--libdir=/usr/lib --enable-nls --with-sysroot=/ --enable-clocale=gnu
--enable-libstdcxx-debug --enable-libstdcxx-time=yes
--enable-gnu-unique-object --enable-plugin --enable-objc-gc
--enable-targets=all --disable-werror --with-arch-32=i686
--with-tune=generic --enable-checking=release --build=i686-linux-gnu
--host=i686-linux-gnu --target=i686-linux-gnu
Thread model: posix
gcc version 4.6.3 (Ubuntu/Linaro 4.6.3-1ubuntu5)
Regards shome
On Thu, Sep 19, 2013 at 6:13 PM, Shomesankar Bhunia <
rightclickatrighttime.gmail.com> wrote:
> Dear Francois,
> My computer is a 32 bit cpu.
> My linux distribution is 32 -bit......ubuntu 12.04 LTS
> my gfortran version is 4.6
>
>
>
>
> On Thu, Sep 19, 2013 at 6:06 PM, FyD <fyd.q4md-forcefieldtools.org> wrote:
>
>> Shomesankar Bhunia,
>>
>> - From your GAMESS output, I saw that your computer cpu is a 32 bit cpu...
>> Could you please confirm?
>>
>> - From your desktop snapshot (picture you sent me) I saw that your
>> Linux distribution is Ubuntu. Could you confirm, & which Ubuntu version?
>>
>> - From the makefile you sent to the Amber mailing list, you used
>> gfortran to compile RESP: which gfortran version, & what do you get
>> when executing 'gfortran -V' ?
>>
>> > You are right. while typing resp in a terminal i am getting a reply
>> "killed".
>> > while installing this i am doing this......
>> >
>> > cd resp-2.2
>> > make clean
>> > make
>>
>> What message do you get after having executed "make"? ... nothing?
>>
>> > su root
>> > cp resp /usr/local/bin/ (moving it to root)
>>
>> -> your install procedure seems ok to me ;-)
>>
>> > after this when I am typing "resp" I am getting a reply "killed"
>> > I am sending you my makefile.
>>
>> So your binary (32 bit; my guess) is not correct...
>>
>> regards, Francois
>>
>>
>> > On Thu, Sep 19, 2013 at 5:42 PM, FyD <fyd.q4md-forcefieldtools.org>
>> wrote:
>> >
>> >> Dear Shomesankar Bhunia,
>> >>
>> >> Thanks for your job/data...
>> >>
>> >> - the espot_m1 (MEP output to the RESP format) & the RESP inputs are
>> >> correctly generated
>> >> - the resp program is found (from the R.E.D. log file)
>> >>
>> >> but the RESP output are not generated: Where are the following output
>> >> files: output1_m1, output2_m1, punch1_m1 & punch2_m1
>> >>
>> >> It looks like the RESP program was not executed by R.E.D., or RESP was
>> >> not successfully compiled on your system...
>> >>
>> >> -1 which RESP version did you use? that available at
>> >> http://q4md-forcefieldtools.org/RED/resp/ or that from the AmberTools?
>> >>
>> >> -2 If I execute 'resp' in a terminal, I get:
>> >> lynx:~/red1> resp
>> >> usage: resp [-O] -i input -o output -p punch -q qin -t qout -e espot
>> >> -w qwts -s esout
>> >>
>> >> do you get a similar message?
>> >> (if not your RESP binary is not correctly compiled).
>> >>
>> >> regards, Francois
>> >>
>> >>
>> >>
>> >> > Did you use the last version of the R.E.D. III.x tools?
>> >> >
>> >> > Could you please send to my personal email address the entire R.E.D.
>> >> > III.x job (compressed archive file) with the Ante_R.E.D. & R.E.D.
>> III.x
>> >> > source codes you used?
>> >> >
>> >> >
>> >> >> I am trying to derive RESP A1 charge for a ligand with Icharge=1. I
>> >> >> generated a GAMESS output (*.log)(generated by AntiRED) and used "
>> >> >> RED-vIII.5.pl" for calculation.
>> >> >> I got the following output.
>> >> >>
>> >> >> =================================================
>> >> >> ======================= Single molecule ===========================
>> >> >> The molecule TITLE is "MOLECULE"
>> >> >> The TOTAL CHARGE value of the molecule is "1"
>> >> >> The SPIN MULTIPLICITY value of the molecule is "1"
>> >> >>
>> >> >>
>> >>
>> ===========================================================================
>> >> >>
>> >> >> * Selected optimization output *
>> >> >> GAMESS
>> >> >> Optimization OUTPUT looks nice !
>> >> >>
>> >> >> * 1 conformation(s) selected *
>> >> >>
>> >> >> WARNING:
>> >> >> A 2nd column of atom names is detected
>> >> >> This 2nd column will be used in the PDB (& Tripos) file(s)
>> >> >>
>> >> >> WARNING:
>> >> >> No three atom based re-orientation found in the P2N file
>> >> >> Re-orientation will be done according to the GAMESS Algorithm!
>> >> >>
>> >> >> * Selected QM Software *
>> >> >> GAMESS
>> >> >>
>> >> >> * Software checking *
>> >> >> gamess.00.x [ OK ]
>> >> >> rungms [ OK ]
>> >> >> ddikick.x [ OK ]
>> >> >> resp [ OK ]
>> >> >>
>> >> >> The Scratch directory defined for GAMESS is /tmp
>> >> >>
>> >> >> Scratch directory for GAMESS [ OK ]
>> >> >>
>> >> >>
>> >> >>
>> >> >> The punch file directory defined for GAMESS is $SCR/$JOB.dat
>> >> >>
>> >> >> MEP(s) is/are being computed for molecule 1 ... [ OK ]
>> >> >> See the file(s) "JOB2-gam_m1-1-(X).log"
>> >> >>
>> >> >> The RESP-A1 charges are being derived for molecule 1 ... [
>> FAILED ]
>> >> >> See the "output(1|2)_m1" file(s)
>> >> >>
>> >> >>
>> >> >> Execution time: 0 h 50 m 3 s
>> >> >>
>> >> >> I looked at the output(1|2)_m1 file but i cant conclude anything.
>> Its
>> >> like
>> >> >> this ( a part of file presented here)
>> >> >>
>> >> >> 51 2249 1 MOLECULE
>> >> >> 3.8981511E+00 -9.6413618E+00 -9.3606430E-01
>> >> >> 4.7466735E+00 -1.1461080E+01 -1.2320434E+00
>> >> >> 5.4224847E+00 -7.5141061E+00 -8.6283949E-01
>> >> >> 7.4220854E+00 -7.7083702E+00 -1.1036052E+00
>> >> >> 4.4816368E+00 -5.0735402E+00 -4.8522919E-01
>> >> >> 1.3078176E+00 -9.4270490E+00 -6.3449774E-01
>> >> >> 7.2522959E-02 -1.1035667E+01 -6.8510030E-01
>> >> >> 3.6637582E-01 -7.0338549E+00 -2.6151893E-01
>> >> >> 1.8661426E+00 -4.8828374E+00 -1.7454598E-01
>> >> >> 9.8373107E-02 -2.7055041E+00 2.7709774E-01
>> >> >> -2.3221161E+00 -3.7062019E+00 4.1801198E-01
>> >> >> -2.3179163E+00 -6.3330989E+00 9.4006139E-02
>> >> >> -4.1328556E+00 -7.6417417E+00 1.0079929E-01
>> >>
>>
>>
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
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Received on Thu Sep 19 2013 - 06:00:06 PDT
