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CNS1.21 with Aria2.2 installation in Mac

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  • cmqian_203
    I am using intel fortran compiler to compile CNS_Solve 1.21 with Aria 2.2 for my iMac OS X 10.6.1. There are several errors coming out when dealt with
    Message 1 of 10 , Nov 2, 2009
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      I am using intel fortran compiler to compile CNS_Solve 1.21 with Aria 2.2 for my iMac OS X 10.6.1. There are several errors coming out when dealt with angledf.f and rama.f. Any suggestions will be appreciated.
      .
      .
      .
      The following are error messages:
      C compiler passes test
      compiling: ifort -traceback -w -vec-report0 -O -axPT
      linking: ifort -static-intel -save-temps -traceback -O -axPT
      Fortran compiler passes test
      making utility programs
      make relink
      make default
      ifort -o PSmapx -O -xP -w -vec-report0 PSmapx.f -i-static
      ifort -o PSmapy -O -xP -w -vec-report0 PSmapy.f -i-static
      ifort -o PSmapz -O -xP -w -vec-report0 PSmapz.f -i-static
      icc -o to_cns -O to_cns.c -lm
      lex refloat.l
      icc -O -o refloat lex.yy.c -lm -lfl
      make clean

      flags:
      fortran -> [ifort] -traceback -w -vec-report0 -O -axPT
      c -> [icc] -O -axPT -DCNS_ARCH_TYPE_LINUX
      link -> [ifort] -static-intel -save-temps -traceback -O -axPT

      compiling: angledb.f
      angledb.f(1453): error #5082: Syntax error, found IDENTIFIER 'NAME' when expecting one of: ( % : . = =>
      CLASSNAME = WD(1:20)
      ---------------------^
      angledb.f(1736): error #5082: Syntax error, found IDENTIFIER 'NAME' when expecting one of: ( % : . = =>
      CLASSNAME = WD(1:20)
      -------------------------------^
      angledb.f(1737): error #5082: Syntax error, found IDENTIFIER 'INDEX' when expecting one of: ( % : . = =>
      CLASSINDEX = 0
      -------------------------------^
      angledb.f(1742): error #5082: Syntax error, found IDENTIFIER 'INDEX' when expecting one of: ( % : . = =>
      CLASSINDEX = COUNT
      -----------------------------------------^
      angledb.f(1453): error #6404: This name does not have a type, and must have an explicit type. [CLASS]
      CLASSNAME = WD(1:20)
      ----------------^
      angledb.f(1453): error #6460: This is not a field name that is defined in the encompassing structure. [NAME]
      CLASSNAME = WD(1:20)
      ---------------------^
      angledb.f(1453): error #6303: The assignment operation or the binary expression operation is invalid for the data types of the two operands. [WD]
      CLASSNAME = WD(1:20)
      ----------------------------^
      angledb.f(1736): error #6303: The assignment operation or the binary expression operation is invalid for the data types of the two operands. [WD]
      CLASSNAME = WD(1:20)
      --------------------------------------^
      angledb.f(1737): error #6460: This is not a field name that is defined in the encompassing structure. [INDEX]
      CLASSINDEX = 0
      -------------------------------^
      compilation aborted for angledb.f (code 1)
      make[3]: *** [angledb.o] Error 1
      compiling: aria.f
      compiling: ariass.f
      compiling: aribac.f
      compiling: arical.f
      compiling: ariman.f
      compiling: arivio.f
      .
      .
      .
    • Axel Brunger
      Which version of ifort are you using? m still running OS 10.5.8 here, but I doubt that s the problem. Try the pre-compiled CNS 1.21 binary for the mac that is
      Message 2 of 10 , Nov 2, 2009
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        Which version of ifort are you using? 

        'm still running OS 10.5.8 here, but I doubt that's the problem. 

        Try the pre-compiled CNS 1.21 binary for the mac that is available on the
        CNS download site.  Make sure you follow the instructions.

        Axel Brunger

        On Nov 2, 2009, at 1:12 PM, cmqian_203 wrote:

        I am using intel fortran compiler to compile CNS_Solve 1.21 with Aria 2.2 for my iMac OS X 10.6.1. There are several errors coming out when dealt with angledf.f and rama.f. Any suggestions will be appreciated.
        .
        .
        .
        The following are error messages:
        C compiler passes test
        compiling: ifort -traceback -w -vec-report0 -O -axPT 
        linking: ifort -static-intel -save-temps -traceback -O -axPT 
        Fortran compiler passes test
        making utility programs
        make relink
        make default
        ifort -o PSmapx -O -xP -w -vec-report0 PSmapx.f -i-static
        ifort -o PSmapy -O -xP -w -vec-report0 PSmapy.f -i-static
        ifort -o PSmapz -O -xP -w -vec-report0 PSmapz.f -i-static
        icc -o to_cns -O to_cns.c -lm
        lex refloat.l
        icc -O -o refloat lex.yy.c -lm -lfl
        make clean

        flags:
        fortran -> [ifort] -traceback -w -vec-report0 -O -axPT 
        c -> [icc] -O -axPT -DCNS_ARCH_TYPE_ LINUX 
        link -> [ifort] -static-intel -save-temps -traceback -O -axPT 

        compiling: angledb.f
        angledb.f(1453) : error #5082: Syntax error, found IDENTIFIER 'NAME' when expecting one of: ( % : . = =>
        CLASSNAME = WD(1:20)
        ------------ --------- ^
        angledb.f(1736) : error #5082: Syntax error, found IDENTIFIER 'NAME' when expecting one of: ( % : . = =>
        CLASSNAME = WD(1:20)
        ------------ --------- --------- -^
        angledb.f(1737) : error #5082: Syntax error, found IDENTIFIER 'INDEX' when expecting one of: ( % : . = =>
        CLASSINDEX = 0
        ------------ --------- --------- -^
        angledb.f(1742) : error #5082: Syntax error, found IDENTIFIER 'INDEX' when expecting one of: ( % : . = =>
        CLASSINDEX = COUNT
        ------------ --------- --------- --------- --^
        angledb.f(1453) : error #6404: This name does not have a type, and must have an explicit type. [CLASS]
        CLASSNAME = WD(1:20)
        ------------ ----^
        angledb.f(1453) : error #6460: This is not a field name that is defined in the encompassing structure. [NAME]
        CLASSNAME = WD(1:20)
        ------------ --------- ^
        angledb.f(1453) : error #6303: The assignment operation or the binary expression operation is invalid for the data types of the two operands. [WD]
        CLASSNAME = WD(1:20)
        ------------ --------- -------^
        angledb.f(1736) : error #6303: The assignment operation or the binary expression operation is invalid for the data types of the two operands. [WD]
        CLASSNAME = WD(1:20)
        ------------ --------- --------- --------^
        angledb.f(1737) : error #6460: This is not a field name that is defined in the encompassing structure. [INDEX]
        CLASSINDEX = 0
        ------------ --------- --------- -^
        compilation aborted for angledb.f (code 1)
        make[3]: *** [angledb.o] Error 1
        compiling: aria.f
        compiling: ariass.f
        compiling: aribac.f
        compiling: arical.f
        compiling: ariman.f
        compiling: arivio.f
        .
        .
        .



        Axel T. Brunger
        Investigator,  Howard Hughes Medical Institute
        Professor of Molecular and Cellular Physiology
        Stanford University

        Email:  brunger@...      
        Phone:  +1 650-736-1031
        Fax:    +1 650-745-1463






      • Chengmin Qian
        Thanks, and I am using Intel fortran/C compiler 11.1.067, the pre-compiled CNS 1.21 binary works fine in my imac, but I need to compile Aria2.2 incorporated
        Message 3 of 10 , Nov 2, 2009
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          Thanks, and I am using Intel fortran/C compiler 11.1.067, the pre-compiled CNS 1.21 binary works fine in my imac, but I need to compile Aria2.2 incorporated CNS1.21 for NMR structure calculation.


          From: Axel Brunger <brunger@...>
          To: cmqian_203 <cmqian_203@...>
          Cc: cnsbb@yahoogroups.com
          Sent: Mon, November 2, 2009 4:58:59 PM
          Subject: Re: [cnsbb] CNS1.21 with Aria2.2 installation in Mac

           

          Which version of ifort are you using? 


          'm still running OS 10.5.8 here, but I doubt that's the problem. 

          Try the pre-compiled CNS 1.21 binary for the mac that is available on the
          CNS download site.  Make sure you follow the instructions.

          Axel Brunger

          On Nov 2, 2009, at 1:12 PM, cmqian_203 wrote:

          I am using intel fortran compiler to compile CNS_Solve 1.21 with Aria 2.2 for my iMac OS X 10.6.1. There are several errors coming out when dealt with angledf.f and rama.f. Any suggestions will be appreciated.
          .
          .
          .
          The following are error messages:
          C compiler passes test
          compiling: ifort -traceback -w -vec-report0 -O -axPT 
          linking: ifort -static-intel -save-temps -traceback -O -axPT 
          Fortran compiler passes test
          making utility programs
          make relink
          make default
          ifort -o PSmapx -O -xP -w -vec-report0 PSmapx.f -i-static
          ifort -o PSmapy -O -xP -w -vec-report0 PSmapy.f -i-static
          ifort -o PSmapz -O -xP -w -vec-report0 PSmapz.f -i-static
          icc -o to_cns -O to_cns.c -lm
          lex refloat.l
          icc -O -o refloat lex.yy.c -lm -lfl
          make clean

          flags:
          fortran -> [ifort] -traceback -w -vec-report0 -O -axPT 
          c -> [icc] -O -axPT -DCNS_ARCH_TYPE_ LINUX 
          link -> [ifort] -static-intel -save-temps -traceback -O -axPT 

          compiling: angledb.f
          angledb.f(1453) : error #5082: Syntax error, found IDENTIFIER 'NAME' when expecting one of: ( % : . = =>
          CLASSNAME = WD(1:20)
          ------------ --------- ^
          angledb.f(1736) : error #5082: Syntax error, found IDENTIFIER 'NAME' when expecting one of: ( % : . = =>
          CLASSNAME = WD(1:20)
          ------------ --------- --------- -^
          angledb.f(1737) : error #5082: Syntax error, found IDENTIFIER 'INDEX' when expecting one of: ( % : . = =>
          CLASSINDEX = 0
          ------------ --------- --------- -^
          angledb.f(1742) : error #5082: Syntax error, found IDENTIFIER 'INDEX' when expecting one of: ( % : . = =>
          CLASSINDEX = COUNT
          ------------ --------- --------- --------- --^
          angledb.f(1453) : error #6404: This name does not have a type, and must have an explicit type. [CLASS]
          CLASSNAME = WD(1:20)
          ------------ ----^
          angledb.f(1453) : error #6460: This is not a field name that is defined in the encompassing structure. [NAME]
          CLASSNAME = WD(1:20)
          ------------ --------- ^
          angledb.f(1453) : error #6303: The assignment operation or the binary expression operation is invalid for the data types of the two operands. [WD]
          CLASSNAME = WD(1:20)
          ------------ --------- -------^
          angledb.f(1736) : error #6303: The assignment operation or the binary expression operation is invalid for the data types of the two operands. [WD]
          CLASSNAME = WD(1:20)
          ------------ --------- --------- --------^
          angledb.f(1737) : error #6460: This is not a field name that is defined in the encompassing structure. [INDEX]
          CLASSINDEX = 0
          ------------ --------- --------- -^
          compilation aborted for angledb.f (code 1)
          make[3]: *** [angledb.o] Error 1
          compiling: aria.f
          compiling: ariass.f
          compiling: aribac.f
          compiling: arical.f
          compiling: ariman.f
          compiling: arivio.f
          .
          .
          .



          Axel T. Brunger
          Investigator,  Howard Hughes Medical Institute
          Professor of Molecular and Cellular Physiology
          Stanford University

          Email:  brunger@stanford. edu      
          Phone:  +1 650-736-1031
          Fax:    +1 650-745-1463







        • Ben Eisenbraun
          Hi Chengmin, ... The ARIA installation notes say two things: - the ARIA CNS routines require CNS version 1.1 - the ARIA routines don t compile on OS X So you
          Message 4 of 10 , Nov 2, 2009
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            Hi Chengmin,

            > Thanks, and I am using Intel fortran/C compiler 11.1.067, the
            > pre-compiled CNS 1.21 binary works fine in my imac, but I need to compile
            > Aria2.2 incorporated CNS1.21 for NMR structure calculation.

            The ARIA installation notes say two things:

            - the ARIA CNS routines require CNS version 1.1
            - the ARIA routines don't compile on OS X

            So you may be out of luck. One of our users wanted to try ARIA, and I just
            built the ARIA bits with the CNS 1.1 source on linux using the Portland
            v9 compiler, which is why this is fresh in my head.

            That combination appears to work okay.

            -ben

            --
            | Ben Eisenbraun | Software Sysadmin |
            | Structural Biology Grid | http://sbgrid.org |
            | Harvard Medical School | http://hms.harvard.edu |
          • Justin Lecher
            Hi all, ... If anyone is interested in using aria released patches with cns 1.2, I adopted the aria patches to apply in the 1.2 cns sources for gentoo linux.
            Message 5 of 10 , Nov 3, 2009
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              Hi all,

              > - the ARIA CNS routines require CNS version 1.1

              If anyone is interested in using aria released patches with cns 1.2, I
              adopted the aria patches to apply in the 1.2 cns sources for gentoo
              linux. Either ask me or fetch the patches from us.

              Cheers justin



              --
              Justin Lecher
              Institute for Neuroscience and Biophysics
              ISB3 - structural biochemistry
              Research Centre Juelich GmbH,
              52425 Juelich,Germany
              phone: +49 2461 61 5385
            • Axel Brunger
              It turns out that this is a feature of the latest ifort compiler. For some reason this compiler has problems with the variable names CLASSNAME and CLASSINDEX
              Message 6 of 10 , Nov 4, 2009
              It turns out that this is a "feature" of the latest ifort compiler.  For some reason
              this compiler has problems with the variable names CLASSNAME and CLASSINDEX that
              are used in the source files angledb.f and rama.f.  

              Attached are files that fix the problem.  Please try again.

              Axel Brunger
            • hussain hussain123
              Dear all, I m trying to fit the inhibitor in the electron density map using* Hic-Up* . but i m facingproblem in converting the doc file to cns readable
              Message 7 of 10 , Dec 2, 2009
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                Dear all,

                I'm trying to fit the inhibitor in the electron density map using Hic-Up . but i'm facingproblem in converting the doc file to cns readable file(cns format) for further refinement.
                   
                     so can any one help me  please...?



                Regards,
                Hussain,

              • Ed Pozharski
                What doc file ? ... --
                Message 8 of 10 , Dec 3, 2009
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                  What "doc file"?

                  On Thu, 2009-12-03 at 10:20 +0530, hussain hussain123 wrote:
                  >
                  > Dear all,
                  >
                  > I'm trying to fit the inhibitor in the electron density map using
                  > Hic-Up . but i'm facingproblem in converting the doc file to cns
                  > readable file(cns format) for further refinement.
                  >
                  > so can any one help me please...?
                  >
                  >
                  >
                  > Regards,
                  > Hussain,
                  >
                  >
                  >
                  >
                  >


                  --
                • Ed Pozharski
                  Are you running CNS on windows? Anyway, my question is what file contains and why do you need to convert it? All the input files for CNS are in plain text.
                  Message 9 of 10 , Dec 4, 2009
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                    Are you running CNS on windows? Anyway, my question is what file
                    contains and why do you need to "convert" it? All the input files for
                    CNS are in plain text.

                    On Fri, 2009-12-04 at 11:47 +0530, hussain hussain123 wrote:
                    > micro soft word file..2003 version


                    --
                  • Tru Huynh
                    ... I can confirm that the attached files are correcting the same issue on our CentOS-5 x86_64 machines. [tru@liberte cns_solve_1.21]$ ifort -V Intel(R)
                    Message 10 of 10 , Dec 8, 2009
                    On Wed, Nov 04, 2009 at 02:53:48PM -0800, Axel Brunger wrote:
                    > It turns out that this is a "feature" of the latest ifort compiler.
                    > For some reason
                    > this compiler has problems with the variable names CLASSNAME and
                    > CLASSINDEX that
                    > are used in the source files angledb.f and rama.f.
                    >
                    > Attached are files that fix the problem. Please try again.

                    I can confirm that the attached files are correcting the same issue on
                    our CentOS-5 x86_64 machines.

                    [tru@liberte cns_solve_1.21]$ ifort -V
                    Intel(R) Fortran Intel(R) 64 Compiler Professional for applications running on Intel(R) 64, Version 11.1 Build 20090827 Package ID: l_cprof_p_11.1.056
                    Copyright (C) 1985-2009 Intel Corporation. All rights reserved.

                    Thanks

                    Tru
                    PS: attached the patch file resulting from diff' ing Axel files
                    and the cns_solve_1.21/source/{angledb,rama}.f files
                    --
                    Dr Tru Huynh | http://www.pasteur.fr/recherche/unites/Binfs/
                    mailto:tru@... | tel/fax +33 1 45 68 87 37/19
                    Institut Pasteur, 25-28 rue du Docteur Roux, 75724 Paris CEDEX 15 France
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