[gmx-users] amber ff and cpp error message

[Florian Haberl]

On Monday 04 September 2006 11:40, Florian Haberl wrote:
> Hi,
>
> i got a strange behaviour of amberff implementation in gromacs
> (http://folding.stanford.edu/ffamber/):
>
> cpp is not running without problems or warnings:

is in faq as e.sorin mailed me 

http://folding.stanford.edu/ffamber/FAQ.html#grompp


>
> checking input for internal consistency...
> calling /lib/cpp...
> In file included
> from /raid1/haberl/bin/gmx/amb_gmx/share/gromacs/top/ffamber03.itp:19,
>                  from topol.top:11:
> /raid1/haberl/bin/gmx/amb_gmx/share/gromacs/top/ffamber03bon.itp:538:22:
> warning: missing whitespace after the macro name
> /raid1/haberl/bin/gmx/amb_gmx/share/gromacs/top/ffamber03bon.itp:540:22:
> warning: missing whitespace after the macro name
> /raid1/haberl/bin/gmx/amb_gmx/share/gromacs/top/ffamber03bon.itp:541:22:
> warning: missing whitespace after the macro name
> /raid1/haberl/bin/gmx/amb_gmx/share/gromacs/top/ffamber03bon.itp:544:21:
> warning: missing whitespace after the macro name
> /raid1/haberl/bin/gmx/amb_gmx/share/gromacs/top/ffamber03bon.itp:555:19:
> warning: missing whitespace after the macro name
> processing topology...
>
> This are the lines from the error or warning message, i would say "*, ' "
> produces them.
>
> ; missing nucleic torsions
> #define proper_X_CT_N*_X  0.00000     0.00000     0.00000     0.00000
> 0.00000     0.00000
> #define proper_X_CM_CT_X   0.00000     0.00000     0.00000     0.00000
> 0.00000     0.00000
> #define proper_X_CK_N*_X  14.22560     0.00000   -14.22560     0.00000
> 0.00000     0.00000
> #define proper_X_CB_N*_X  13.80720     0.00000   -13.80720     0.00000
> 0.00000     0.00000
> #define proper_X_CA_NC_X  40.16640     0.00000   -40.16640     0.00000
> 0.00000     0.00000
> #define proper_X_CQ_NC_X  56.90240     0.00000   -56.90240     0.00000
> 0.00000     0.00000
>
> is this a normal behaviour?
>
> OS is suse 10.1 running on x86_64
>
> cpp -v
> Using built-in specs.
> Target: x86_64-suse-linux
> Configured with: ../configure --enable-threads=posix --prefix=/usr
> --with-local-prefix=/usr/local --infodir=/usr/share/info
> --mandir=/usr/share/man --libdir=/usr/lib64 --libexecdir=/usr/lib64
> --enable-languages=c,c++,objc,fortran,java,ada --enable-checking=release
> --with-gxx-include-dir=/usr/include/c++/4.1.0 --enable-ssp --disable-libssp
> --enable-java-awt=gtk --enable-gtk-cairo --disable-libjava-multilib
> --with-slibdir=/lib64 --with-system-zlib --enable-shared
> --enable-__cxa_atexit --enable-libstdcxx-allocator=new
> --without-system-libunwind --with-cpu=generic --host=x86_64-suse-linux
> Thread model: posix
> gcc version 4.1.0 (SUSE Linux)
>  /usr/lib64/gcc/x86_64-suse-linux/4.1.0/cc1 -E -quiet -v - -mtune=generic
> #include "..." search starts here:
> #include <...> search starts here:
>  /usr/local/include
>  /usr/lib64/gcc/x86_64-suse-linux/4.1.0/include
> 
> /usr/lib64/gcc/x86_64-suse-linux/4.1.0/../../../../x86_64-suse-linux/includ
>e /usr/include
> End of search list
>
> Greetings,
>
> Florian

-- 
-------------------------------------------------------------------------------
 Florian Haberl                        
 Computer-Chemie-Centrum   
 Universitaet Erlangen/ Nuernberg
 Naegelsbachstr 25
 D-91052 Erlangen
 Telephone:  	+49(0) − 9131 − 85 26581
 Mailto: florian.haberl AT chemie.uni-erlangen.de
-------------------------------------------------------------------------------