Subject: Autodock 3.0.5 compile dies on Linux... ???

From: Kenward Vaughan <[email-masked]>
Date: Sat, 21 Apr 2001 13:21:33 -0700

Hello,

I've just tried compiling v. 3.0.5 on my Debian box (Athlon cpu, FWIW) and
the linking stage died on me. My Makefile was a duplicate of the suggested
Linux changes found on the site off of the Autodock page. I also tried
compiling autogrid--it gets toasted too.

(The _real_ problem is that I am not a programmer, so my efforts die there
as well.  :-( )

Has someone been through this and/or can help me with these things?  I am
very interested in using Autodock as a part of a demo to my community
college administrators to support a grant request for computers in the
department.  It hopefully would become a staple of the independent study
program I want to offer my advanced students, too.

I have attached excerpts of the Makefile and compiling messages autodock. 
If this can be worked out I would like to try addressing the problem with
autogrid as well, if the kind soul is willing.  :)

Thanks very much,

Kenward Vaughan
[email-masked]  (home)

---snippet of Makefile---
...
#
# C++ compiler
#

# AutoDock 3.0 Makefile GNU Linux -- START
CC        = g++
LIB       = -lm
CSTD      = -DHPPA $(PROF) $(DBUG) $(WARN)
CFLAGS    = $(OPT)
OPTLEVEL  = -O3
OPT       = $(CSTD) $(OPTLEVEL)
OLIMIT    = $(OPT)
LINKOPT   = $(OPT)
LINK      = $(LINKOPT)
LINT      = lint
LINTFLAGS = -DHPPA $(LIB) -c
DBUG      = -DNDEBUG # No debugging and no assert code
PROF      = # No profiling
WARN      = # Default warning level
# AutoDock 3.0 Makefile GNU Linux -- END

autodock3 : main.o $(ADLIB)
...

---errors in compiling messages---I don't believe the warnings are
	important?  Sorry about the line wrap...

...
g++ -DHPPA  -DNDEBUG   -O3 -c getpdbcrds.cc
g++ -DHPPA  -DNDEBUG   -O3 -DCHECK_ISNAN -c gs.cc -o gs.o
gs.cc: In method enetic_Algorithm::Genetic_Algorithm(EvalMode,
Selection_Mode, Xover_Mode, Worst_Mode, int, float, float, int, unsigned
int, unsigned int)':
gs.cc:170: warning: assignment to 	nt' from ouble'
gs.cc:170: warning: assignment to 	nt' from ouble'
...

g++ -DHPPA  -DNDEBUG   -O3 -c ranlib.cc
ranlib.cc: In function ourByteLong ignbin(long int, float)':
ranlib.cc:766: warning: assignment to ourByteLong' from loat'
ranlib.cc:791: warning: assignment to ourByteLong' from loat'
ranlib.cc:801: warning: assignment to ourByteLong' from loat'
ranlib.cc:808: warning: assignment to ourByteLong' from ouble'
ranlib.cc:816: warning: assignment to ourByteLong' from ouble'
...

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
echo . '  on  'ate', using 'ostname >> 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
./libad.a(clmode.o): In function lmode(char *, int, float, char *, long,
tms,
char, char *, float (*)[2], float *, char, char *)':
clmode.o(.text+0x640): undefined reference to et_atom_type(char *, char *)'
./libad.a(cmdmode.o): In function mdmode(int, long, tms, float, float,
float,
float, float, float, float, float (*)[127][127][7], float (*)[5][5], float,
float (*)[2], int (*)[2047], int, int, int (*)[1], char (*)[127], float
(*)[2], char *, int *, float *, char, float *, char *, float, int)':
cmdmode.o(.text+0x48f): undefined reference to et_atom_type(char *, char
*)'
./libad.a(readPDBQ.o): In function eadPDBQ(char *, char *, int, int *,
float (*)[2], float *, char *, int *, char (*)[4], char *,
_ciT0T3T3T5T5T3T3PA2047_iT4
(*)[1], int *, int *, int (*)[1], long, tms, char *, int *)':
readPDBQ.o(.text+0x465): undefined reference to et_atom_type(char *, char
*)'
collect2: ld returned 1 exit status
make: *** [autodock3] Error 1

---end of run---

-- 
                                          .'^~;,_
Dr. Kenward Vaughan                       `:,'~~~~~
Professor of Chemistry                    \;:/
Bakersfield College                       |,;|
Bakersfield, CA  93305                   / ', \
661-395-4243                            / o  O \
[email-masked]                   (oOoOOoOo)
                                     ---========---
                                      ???$$MM$$???