ADL: can the max number of grid points exceed 128?

Madalin Giambasu giambasu at biochim.ro
Wed Sep 22 01:27:05 PDT 2004


Dear James (zhangrui1002 at 163.com) and autodockers,


I managed to recompile autogrid for 400 grid points and all went very
well. Unfortunately the copilation of autodock doesnot lead to a
functional binary ( I got a "segmentation fault" even if I set the
stacksize). The only variable I changed is MAX_GRID_PTS to 400 (from 128)
in the three files autocomm* from /src/autodock and /src/autogrid
directories.

The compilation of autodock3 leads to the following output. If there are
more experienced programmers, please help to see what is wrong:

make -f Makefile.autodock
g++ -DHPPA  -DNDEBUG   -O3 -c -DWRITEPDBQSTATE main.cc
In file included from /usr/include/c++/3.2.2/backward/iostream.h:31,
                 from main.cc:3:
/usr/include/c++/3.2.2/backward/backward_warning.h:32:2: warning: #warning
This file includes at least one deprecated
or antiquated header. Please consider using one of the 32 headers found in
section 17.4.1.2 of the C++ standard. Examples include substituting the
<X> header for the <X.h> header for C++ includes, or <sstream> instead of
the deprecated
header <strstream.h>. To disable this warning use -Wno-deprecated.
g++ -DHPPA  -DNDEBUG   -O3 -c analysis.cc
g++ -DHPPA  -DNDEBUG   -O3 -c banner.cc
g++ -DHPPA  -DNDEBUG   -O3 -c bestpdb.cc
g++ -DHPPA  -DNDEBUG   -O3 -c call_glss.cc
In file included from /usr/include/c++/3.2.2/backward/iostream.h:31,
                 from call_glss.cc:11:
/usr/include/c++/3.2.2/backward/backward_warning.h:32:2: warning: #warning
This file includes at least one deprecated
or antiquated header. Please consider using one of the 32 headers found in
section 17.4.1.2 of the C++ standard. Examples include substituting the
<X> header for the <X.h> header for C++ includes, or <sstream> instead of
the deprecated
header <strstream.h>. To disable this warning use -Wno-deprecated.
g++ -DHPPA  -DNDEBUG   -O3 -c call_gs.cc
In file included from /usr/include/c++/3.2.2/backward/iostream.h:31,
                 from call_gs.cc:8:
/usr/include/c++/3.2.2/backward/backward_warning.h:32:2: warning: #warning
This file includes at least one deprecated
or antiquated header. Please consider using one of the 32 headers found in
section 17.4.1.2 of the C++ standard. Examples include substituting the
<X> header for the <X.h> header for C++ includes, or <sstream> instead of
the deprecated
header <strstream.h>. To disable this warning use -Wno-deprecated.
g++ -DHPPA  -DNDEBUG   -O3 -c call_ls.cc
In file included from /usr/include/c++/3.2.2/backward/iostream.h:31,
                 from call_ls.cc:9:
/usr/include/c++/3.2.2/backward/backward_warning.h:32:2: warning: #warning
This file includes at least one deprecated
or antiquated header. Please consider using one of the 32 headers found in
section 17.4.1.2 of the C++ standard. Examples include substituting the
<X> header for the <X.h> header for C++ includes, or <sstream> instead of
the deprecated
header <strstream.h>. To disable this warning use -Wno-deprecated.
g++ -DHPPA  -DNDEBUG   -O3 -c changeState.cc
g++ -DHPPA  -DNDEBUG   -O3 -c check_header_float.cc
g++ -DHPPA  -DNDEBUG   -O3 -c check_header_int.cc
g++ -DHPPA  -DNDEBUG   -O3 -c check_header_line.cc
g++ -DHPPA  -DNDEBUG   -O3 -c cluster_analysis.cc
g++ -DHPPA  -DNDEBUG   -O3 -c clmode.cc
g++ -DHPPA  -DNDEBUG   -O3 -c -DEINTCALPRINT cmdmode.cc
g++ -DHPPA  -DNDEBUG   -O3 -c cnv_state_to_coords.cc
g++ -DHPPA  -DNDEBUG   -O3 -c com.cc
g++ -DHPPA  -DNDEBUG   -O3 -c stateLibrary.cc
g++ -DHPPA  -DNDEBUG   -O3 -c readfield.cc
g++ -DHPPA  -DNDEBUG   -O3 -c readmap.cc
g++ -DHPPA  -DNDEBUG   -O3 -c readPDBQ.cc
g++ -DHPPA  -DNDEBUG   -O3 -c dpftypes.cc
g++ -DHPPA  -DNDEBUG   -O3 -c eval.cc
In file included from /usr/include/c++/3.2.2/backward/iostream.h:31,
                 from rep.h:16,
                 from eval.h:9,
                 from eval.cc:9:
/usr/include/c++/3.2.2/backward/backward_warning.h:32:2: warning: #warning
This file includes at least one deprecated
or antiquated header. Please consider using one of the 32 headers found in
section 17.4.1.2 of the C++ standard. Examples include substituting the
<X> header for the <X.h> header for C++ includes, or <sstream> instead of
the deprecated
header <strstream.h>. To disable this warning use -Wno-deprecated.
g++ -DHPPA  -DNDEBUG   -O3 -c evaluate_energy.cc
g++ -DHPPA  -DNDEBUG   -O3 -c gencau.cc
g++ -DHPPA  -DNDEBUG   -O3 -c getrms.cc
g++ -DHPPA  -DNDEBUG   -O3 -c get_atom_type.cc
g++ -DHPPA  -DNDEBUG   -O3 -c getInitialState.cc
g++ -DHPPA  -DNDEBUG   -O3 -c getpdbcrds.cc
g++ -DHPPA  -DNDEBUG   -O3 -DCHECK_ISNAN -c gs.cc -o gs.o
In file included from /usr/include/c++/3.2.2/backward/iostream.h:31,
                 from gs.cc:7:
/usr/include/c++/3.2.2/backward/backward_warning.h:32:2: warning: #warning
This file includes at least one deprecated
or antiquated header. Please consider using one of the 32 headers found in
section 17.4.1.2 of the C++ standard. Examples include substituting the
<X> header for the <X.h> header for C++ includes, or <sstream> instead of
the deprecated
header <strstream.h>. To disable this warning use -Wno-deprecated.
gs.cc: In constructor `Genetic_Algorithm::Genetic_Algorithm(EvalMode,
   Selection_Mode, Xover_Mode, Worst_Mode, int, float, float, int,
unsigned
   int, unsigned int)':
gs.cc:170: warning: initialization to `int' from `double'
gs.cc:170: warning: argument to `int' from `double'
gs.cc:170: warning: initialization to `int' from `double'
gs.cc:170: warning: argument to `int' from `double'
g++ -DHPPA  -DNDEBUG   -O3 -c initautodock.cc
g++ -DHPPA  -DNDEBUG   -O3 -c input_state.cc
g++ -DHPPA  -DNDEBUG   -O3 -c investigate.cc
g++ -DHPPA  -DNDEBUG   -O3 -c linpack.cc
g++ -DHPPA  -DNDEBUG   -O3 -c ls.cc
In file included from /usr/include/c++/3.2.2/backward/iostream.h:31,
                 from rep.h:16,
                 from support.h:20,
                 from ls.h:14,
                 from ls.cc:8:
/usr/include/c++/3.2.2/backward/backward_warning.h:32:2: warning: #warning
This file includes at least one deprecated
or antiquated header. Please consider using one of the 32 headers found in
section 17.4.1.2 of the C++ standard. Examples include substituting the
<X> header for the <X.h> header for C++ includes, or <sstream> instead of
the deprecated
header <strstream.h>. To disable this warning use -Wno-deprecated.
g++ -DHPPA  -DNDEBUG   -O3 -c mapping.cc
In file included from /usr/include/c++/3.2.2/backward/iostream.h:31,
                 from rep.h:16,
                 from support.h:20,
                 from mapping.cc:7:
/usr/include/c++/3.2.2/backward/backward_warning.h:32:2: warning: #warning
This file includes at least one deprecated
or antiquated header. Please consider using one of the 32 headers found in
section 17.4.1.2 of the C++ standard. Examples include substituting the
<X> header for the <X.h> header for C++ includes, or <sstream> instead of
the deprecated
header <strstream.h>. To disable this warning use -Wno-deprecated.
g++ -DHPPA  -DNDEBUG   -O3 -c minmeanmax.cc
In file included from /usr/include/c++/3.2.2/backward/iostream.h:31,
                 from rep.h:16,
                 from minmeanmax.cc:8:
/usr/include/c++/3.2.2/backward/backward_warning.h:32:2: warning: #warning
This file includes at least one deprecated
or antiquated header. Please consider using one of the 32 headers found in
section 17.4.1.2 of the C++ standard. Examples include substituting the
<X> header for the <X.h> header for C++ includes, or <sstream> instead of
the deprecated
header <strstream.h>. To disable this warning use -Wno-deprecated.
g++ -DHPPA  -DNDEBUG   -O3 -c mkNewState.cc
g++ -DHPPA  -DNDEBUG   -O3 -c mkTorTree.cc
g++ -DHPPA  -DNDEBUG   -O3 -c mkRandomState.cc
g++ -DHPPA  -DNDEBUG   -O3 -c nonbonds.cc
g++ -DHPPA  -DNDEBUG   -O3 -c openfile.cc
g++ -DHPPA  -DNDEBUG   -O3 -c output_state.cc
g++ -DHPPA  -DNDEBUG   -O3 -c parse_com_line.cc
g++ -DHPPA  -DNDEBUG   -O3 -c parse_dpf_line.cc
g++ -DHPPA  -DNDEBUG   -O3 -c parse_pdbq_line.cc
g++ -DHPPA  -DNDEBUG   -O3 -c parse_trj_line.cc
g++ -DHPPA  -DNDEBUG   -O3 -c print_2x.cc
g++ -DHPPA  -DNDEBUG   -O3 -c print_atomic_energies.cc
g++ -DHPPA  -DNDEBUG   -O3 -c print_avsfld.cc
g++ -DHPPA  -DNDEBUG   -O3 -c -DWRITEMOLASPDBQFUNC writePDBQ.cc -o
writeMolAsPDBQ.o
g++ -DHPPA  -DNDEBUG   -O3 -c writePDBQ.cc -o writePDBQ.o
g++ -DHPPA  -DNDEBUG   -O3 -c -DWRITEPDBQSTATE writePDBQ.cc -o
writePDBQState.o
g++ -DHPPA  -DNDEBUG   -O3 -c print_rem.cc
g++ -DHPPA  -DNDEBUG   -O3 -c printdate.cc
g++ -DHPPA  -DNDEBUG   -O3 -c printEnergies.cc
g++ -DHPPA  -DNDEBUG   -O3 -c printhms.cc
g++ -DHPPA  -DNDEBUG   -O3 -c prClusterHist.cc
g++ -DHPPA  -DNDEBUG   -O3 -c prInitialState.cc
g++ -DHPPA  -DNDEBUG   -O3 -c prTorConList.cc
g++ -DHPPA  -DNDEBUG   -O3 -c qmultiply.cc
g++ -DHPPA  -DNDEBUG   -O3 -c qtransform.cc
g++ -DHPPA  -DNDEBUG   -O3 -c quicksort.cc
g++ -DHPPA  -DNDEBUG   -O3 -c ranlib.cc
ranlib.cc: In function `FourByteLong ignbin(long int, float)':
ranlib.cc:766: warning: assignment to `FourByteLong' from `float'
ranlib.cc:766: warning: argument to `long int' from `float'
ranlib.cc:791: warning: assignment to `FourByteLong' from `float'
ranlib.cc:791: warning: argument to `long int' from `float'
ranlib.cc:801: warning: assignment to `FourByteLong' from `float'
ranlib.cc:801: warning: argument to `long int' from `float'
ranlib.cc:808: warning: assignment to `FourByteLong' from `double'
ranlib.cc:808: warning: argument to `long int' from `double'
ranlib.cc:816: warning: assignment to `FourByteLong' from `double'
ranlib.cc:816: warning: argument to `long int' from `double'
g++ -DHPPA  -DNDEBUG   -O3 -c rep.cc
In file included from /usr/include/c++/3.2.2/backward/iostream.h:31,
                 from rep.cc:9:
/usr/include/c++/3.2.2/backward/backward_warning.h:32:2: warning: #warning
This file includes at least one deprecated
or antiquated header. Please consider using one of the 32 headers found in
section 17.4.1.2 of the C++ standard. Examples include substituting the
<X> header for the <X.h> header for C++ includes, or <sstream> instead of
the deprecated
header <strstream.h>. To disable this warning use -Wno-deprecated.
g++ -DHPPA  -DNDEBUG   -O3 -c scauchy.cc
g++ -DHPPA  -DNDEBUG   -O3 -c set_cmd_io_std.cc
g++ -DHPPA  -DNDEBUG   -O3 -c setflags.cc
g++ -DHPPA  -DNDEBUG   -O3 -c simanneal.cc
g++ -DHPPA  -DNDEBUG   -O3 -c sort_enrg.cc
g++ -DHPPA  -DNDEBUG   -O3 -c stop.cc
g++ -DHPPA  -DNDEBUG   -O3 -c strindex.cc
g++ -DHPPA  -DNDEBUG   -O3 -c success.cc
g++ -DHPPA  -DNDEBUG   -O3 -c summarizegrids.cc
g++ -DHPPA  -DNDEBUG   -O3 -c support.cc
In file included from /usr/include/c++/3.2.2/backward/iostream.h:31,
                 from rep.h:16,
                 from eval.h:9,
                 from support.cc:7:
/usr/include/c++/3.2.2/backward/backward_warning.h:32:2: warning: #warning
This file includes at least one deprecated
or antiquated header. Please consider using one of the 32 headers found in
section 17.4.1.2 of the C++ standard. Examples include substituting the
<X> header for the <X.h> header for C++ includes, or <sstream> instead of
the deprecated
header <strstream.h>. To disable this warning use -Wno-deprecated.
g++ -DHPPA  -DNDEBUG   -O3 -c swap.cc
g++ -DHPPA  -DNDEBUG   -O3 -c timesys.cc
g++ -DHPPA  -DNDEBUG   -O3 -c timesyshms.cc
g++ -DHPPA  -DNDEBUG   -O3 -c torNorVec.cc
g++ -DHPPA  -DNDEBUG   -O3 -c torsion.cc
g++ -DHPPA  -DNDEBUG   -O3 -c usage.cc
g++ -DHPPA  -DNDEBUG   -O3 -c weedbonds.cc
g++ -DHPPA  -DNDEBUG   -O3 -c warn_bad_file.cc
g++ -DHPPA  -DNDEBUG   -O3 -DNOSQRT -DBOUNDED -c eintcal.cc -o eintcal.o
g++ -DHPPA  -DNDEBUG   -O3 -DNOSQRT -DBOUNDED -DEINTCALPRINT -c eintcal.cc
-o eintcalPrint.o
g++ -DHPPA  -DNDEBUG   -O3 -DNOSQRT -c intnbtable.cc
g++ -DHPPA  -DNDEBUG   -O3 -DNOSQRT -c nbe.cc
g++ -DHPPA  -DNDEBUG   -O3 -c trilinterp.cc
ar r  libad.a analysis.o banner.o bestpdb.o call_glss.o call_gs.o
call_ls.o changeState.o check_header_float.o check_header_int.o
check_header_line.o cluster_analysis.o clmode.o cmdmode.o
cnv_state_to_coords.o com.o stateLibrary.o readfield.o readmap.o
readPDBQ.o dpftypes.o eval.o evaluate_energy.o gencau.o getrms.o
get_atom_type.o getInitialState.o getpdbcrds.o gs.o initautodock.o
input_state.o investigate.o linpack.o ls.o mapping.o minmeanmax.o
mkNewState.o mkTorTree.o mkRandomState.o nonbonds.o openfile.o
output_state.o parse_com_line.o parse_dpf_line.o parse_pdbq_line.o
parse_trj_line.o print_2x.o print_atomic_energies.o print_avsfld.o
writeMolAsPDBQ.o writePDBQ.o writePDBQState.o print_rem.o printdate.o
printEnergies.o printhms.o prClusterHist.o prInitialState.o prTorConList.o
qmultiply.o qtransform.o quicksort.o ranlib.o rep.o scauchy.o
set_cmd_io_std.o setflags.o simanneal.o sort_enrg.o stop.o strindex.o
success.o summarizegrids.o support.o swap.o timesys.o timesyshms.o
torNorVec.o torsion.o usage.o weedbonds.o warn_bad_file.o eintcal.o
eintcalPrint.o intnbtable.o nbe.o trilinterp.o
ranlib   libad.a
echo . '  on  '`date`', using '`hostname` >> LATEST_MAKE
echo 'Flags: 'g++ -DHPPA  -DNDEBUG   -O3 -DNOSQRT -L. -lad -lm >>
LATEST_MAKE
g++ -DHPPA  -DNDEBUG   -O3 -DNOSQRT -o autodock3 main.o -L. -lad -lm


-------------------------------------------------------
Madalin G. Giambasu
Junior Research Assistant
Institute of Biochemistry of Romanian Academy of Science
Splaiul Independentei 296, 060031, Bucharest 17, Romania
Phone: (+4)021.223.90.69; FAX: (+4)021.223.90.68

-------------------------------------------------------

On Thu, 20 May 2004, [gb2312] zhangrui1002 wrote:

> Dear dockers,
>    the default maximum number of grid points is set to 128. and now I have to reset it to more than 200, e.g 256. I`ve just changed this value written in all the related files under the dir of src including autocomm.h, autocom.h-extra-maps and autocomm.h under dir of autodock. After that I recoplied the file under these two dirs and copied the binary files under the dir of share.
>    But when I excecuted autogrid3, stil the max number was 128 which was in grid log file.
>    so can the max number of grid points exceed 128?
>    Thanks in advance for your help. 
>        cheers
>            yours James
> ========================================================
> ÕæÇé»ØÀ¡ ³¬ÖµÓÅ»Ý VIPÓÊÏäÂòÒ»ËÍËÄ ÂòÈýËÍÊ®¶þ£¡       http://vip.163.com
> Öйú×î´óµÄÃâ·ÑÓÊÏäÔÚµÈÄã 25Õ׿ռä4Õ׸½¼þ£¡¡¡¡¡¡¡¡¡¡¡ http://mail.163.com
> µã»÷ÍøÒ×ÅÝÅݾªÏ²ÎÞÏÞ È«Ãâ·ÑÊÖ»ú¶ÌÐÅÈÎÄã·¢!¡¡¡¡¡¡¡¡   http://popo.163.com
> ________________________________________________
> --- ADL: AutoDock List  --- http://www.scripps.edu/pub/olson-web/doc/autodock/ ---
> 





More information about the autodock mailing list