Subject: Compilation problem - Autodock 3.0 - ATOM_MAPS variable in autoco mm.h

From: [email-masked]
Date: Fri, 26 Jul 2002 15:40:16 -0400

Hello CCLers,

I have a perplexing problem, and I'd like to give more details about what I
posted before.

1) The autodock3 binary only handles 6 atom types by default. I was able to
compile this okay.

2) When I try to call the program using acetyl-CoA as a ligand, it crashes,
telling me to recompile, changing the ATOM_MAPS variable in autocomm.h.

3) When I change this variable, it fails to compile and gives error messages
of the type:

[donald@localhost autodock]$ make
gcc  -DNDEBUG     -O3    -c -DWRITEPDBQSTATE main.cc
gcc  -DNDEBUG     -O3    -c call_gs.cc
gcc  -DNDEBUG     -O3    -c -DEINTCALPRINT cmdmode.cc
gcc  -DNDEBUG     -O3    -c readmap.cc
gcc  -DNDEBUG     -O3    -c readPDBQ.cc
gcc  -DNDEBUG     -O3    -c eval.cc
gcc  -DNDEBUG     -O3    -c getrms.cc
gcc  -DNDEBUG     -O3    -c getInitialState.cc
gcc  -DNDEBUG     -O3    -c initautodock.cc
gcc  -DNDEBUG     -O3    -c openfile.cc
gcc  -DNDEBUG     -O3    -c -DWRITEMOLASPDBQFUNC writePDBQ.cc -o
writeMolAsPDBQ.o
gcc  -DNDEBUG     -O3    -c writePDBQ.cc -o writePDBQ.o
gcc  -DNDEBUG     -O3    -c -DWRITEPDBQSTATE writePDBQ.cc -o
writePDBQState.o
gcc  -DNDEBUG     -O3    -c prTorConList.cc
gcc  -DNDEBUG     -O3    -c simanneal.cc
gcc  -DNDEBUG     -O3    -c success.cc
gcc  -DNDEBUG     -O3    -c summarizegrids.cc
ar r  libad.a call_gs.o cmdmode.o readmap.o readPDBQ.o eval.o getrms.o
getInitialState.o initautodock.o openfile.o writeMolAsPDBQ.o writePDBQ.o
writePDBQState.o prTorConList.o simanneal.o success.o summarizegrids.o
ranlib   libad.a
echo /usr/local/autodock3/bin '  on  '`date`', using '`hostname` >>
LATEST_MAKE
echo 'Flags: 'gcc  -DNDEBUG     -O3     -DNOSQRT -L. -lad -lm  >>
LATEST_MAKE
gcc  -DNDEBUG     -O3     -DNOSQRT -o autodock3 main.o -L. -lad -lm 
main.o: In function `main':
main.o(.text+0x1921): undefined reference to
`intnbtable__FPcPiT1iT0ffiiPA13_A13_f'
main.o(.text+0x303f): undefined reference to `nbe(char *, _A1 (*)[1], _fi)'
main.o(.text+0x538d): undefined reference to
`analysis__FiPA127_cPfcT2fPA2_fPA13_A13_ffPA127_A127_A15_fT2ifffiPA1_iiiP5st
atePcT2cPA2047_iPiT6T20_fcicT2T2'
main.o(.text+0x55a9): undefined reference to
`investigate__FiPfcT1PA2_fT4PA13_A13_fffffifffPA127_A127_A15_fiPA1_iiiPA2047
_iPiT4cPA255_UsPccPUsPA7_A1_fT21_cT25_iiff'
./libad.a(cmdmode.o): In function
`cmdmode__FilG3tmsfffffffPA127_A127_A15_fPA13_A13_ffPA2_fPA2047_iiiPA1_iPA12
7_cT13_PcPiPfcT22_T20_fi':
.
.
.
getInitialState.o(.text+0x4fd): undefined reference to `eintcal(int (*)[1],
_A1 (*)[1], _fP, float [2], int *, int, char, float *)'
collect2: ld returned 1 exit status
make: *** [autodock3] Error 1

4) I have been in touch with Robert Flight and tried his workaround using
"autocomm.h-extra-maps". It is sucessful in compiling a new version of
autogrid, but autodock3 still fails as above. Changing the variable by hand
also causes the compile to fail.

5) If I change autocomm.h back to its default state, autodock3 compiles
perfectly.

Does anyone know what is happening here? Is there some sort of file or
variable interdependency that I am missing? Thank you for any light you may
shed on my situation.

Sincerely,
Donald Choi, Ph.D.
Harvard Medical School
[email-masked]