Re: AMBER: How to compile antechamber?

From: Julien Michel <j.michel.soton.ac.uk>
Date: Fri, 26 Mar 2004 10:35:11 +0000

Hi,

I managed to compile the antechamber source code for linux RH9.0 with the
makefile attached below. I am not really sure however that this release of
antechamber is fully functional without the release of amber8. I had to copy
the exe and dat files in my amber7 directory to be able to run the simple file
conversion operations because the source relies on the environment variable
$AMBERHOME to locate executables.
When I tried to use antechamber to generate bcc charges I got the following
error message :

test>../../amber7/exe/antechamber -i butane.mol2 -fi mol2 -o butane.prepi -fo
prepi -c bcc

Total number of electrons: 34; net charge: 0

Running: /home/julien/software/amber7//exe/divcon
sh: line 1: /home/julien/software/amber7//exe/divcon: No such file or
directory Cannot open divcon.out , exit

Inspection of the source code suggest that divcon is an executable that calls
mopac to perform the AM1 calculation. It is not part of the amber7 release
(where mopac was called with a shell script) and was not included in the
antechamber source code either. I suppose somebody forgot to include it in the
release ?

-- 
Julien Michel
University of Southampton
Department of Chemistry
Dr J. W. Essex group 
---------------------------------------------------------------------
# makefile for antechamber
PROGS = \
	am1bcc \
	antechamber\
	atomtype \
	bondtype \
	crdgrow \
	database \
	espgen \
	parmcal \
	parmchk \
	prepgen \
	respgen 
#############################################################################
install: all
	mv $(PROGS) ../exe
all: $(PROGS)
clean:
	-rm -f *.o $(PROGS)
#############################################################################
#_____________________________________________________________________________
# Dependencies, for ./makedepend:
am1bcc.o: common.h
am1bcc.o: define.h
am1bcc.o: atom.h
am1bcc.o: common.c
am1bcc.o: rotate.c
am1bcc.o: ac.c
am1bcc.o: pdb.c
antechamber.o: common.h
antechamber.o: define.h
antechamber.o: atom.h
antechamber.o: common.c
antechamber.o: ring.c
antechamber.o: rotate.c
antechamber.o: ac.c
antechamber.o: mol2.c
antechamber.o: mopcrt.c
antechamber.o: mopint.c
antechamber.o: mopout.c
antechamber.o: gcrt.c
antechamber.o: gzmat.c
antechamber.o: gout.c
antechamber.o: pdb.c
antechamber.o: csd.c
antechamber.o: mdl.c
antechamber.o: alc.c
antechamber.o: hin.c
antechamber.o: prep.c
antechamber.o: rst.c
antechamber.o: charge.c
atomtype.o: common.h
atomtype.o: define.h
atomtype.o: atom.h
atomtype.o: common.c
atomtype.o: ring.c
atomtype.o: rotate.c
atomtype.o: ac.c
atomtype.o: mol2.c
crdgrow.o: common.h
crdgrow.o: define.h
crdgrow.o: atom.h
crdgrow.o: common.c
crdgrow.o: rotate.c
crdgrow.o: pdb.c
crdgrow.o: ac.c
crdgrow.o: prep.c
database.o: define.h
database.o: common.h
database.o: atom.h
database.o: common.c
delphigen.o: common.h
delphigen.o: define.h
delphigen.o: atom.h
delphigen.o: common.c
delphigen.o: ac.c
delphigen.o: pdb.c
espgen.o: common.h
espgen.o: define.h
espgen.o: atom.h
parmcal.o: common.h
parmcal.o: define.h
parmchk.o: common.h
parmchk.o: define.h
parmchk.o: atom.h
parmchk.o: common.c
parmchk.o: rotate.c
parmchk.o: ac.c
parmchk.o: mol2.c
parmchk.o: prep.c
parmjoin.o: common.h
parmjoin.o: define.h
prepgen.o: common.h
prepgen.o: define.h
prepgen.o: atom.h
prepgen.o: common.c
prepgen.o: rotate.c
prepgen.o: ring.c
prepgen.o: ac.c
respgen.o: common.h
respgen.o: define.h
respgen.o: atom.h
respgen.o: common.c
respgen.o: ac.c
rotate.o: common.h
smiles.o: common.h
smiles.o: define.h
smiles.o: atom.h
smiles.o: globals.h
utility.o: common.h
utility.o: define.h
utility.o: atom.h
utility.o: globals.h
#_____________________________________________________________________________
# Programs
CC = gcc
CFLAGS = -O2
CPLUSPLUS = g++
CPPFLAGS = -O2
MATHS = -lm
 
am1bcc : am1bcc.o 
	$(CC) $(CFLAGS) $(MATHS) am1bcc.o -o am1bcc
antechamber: antechamber.o
	$(CC) $(CFLAGS) $(MATHS) antechamber.o -o antechamber
atomtype : atomtype.o
	$(CC) $(CFLAGS) $(MATHS) atomtype.o -o atomtype
bondtype.o: bondtype.C
	$(CPLUSPLUS) -c $(CPPFLAGS) -o bondtype.o bondtype.C
bondtype: bondtype.o
	$(CPLUSPLUS) $(MATHS) bondtype.o -o bondtype
crdgrow: crdgrow.o
	$(CC) $(CFLAGS) $(MATHS) crdgrow.o -o crdgrow
database: database.o
	$(CC) $(CFLAGS) $(MATHS) database.o -o database
delphigen: delphigen.o
	$(CC) $(CFLAGS) delphigen.o -o delphigen
espgen: espgen.o
	$(CC) $(CFLAGS) espgen.o -o espgen
parmcal: parmcal.o 
	$(CC) $(CFLAGS) $(MATHS) parmcal.o -o parmcal
parmchk: parmchk.o 
	$(CC) $(CFLAGS) $(MATHS) parmchk.o -o parmchk
parmjoin: parmjoin.o 
	$(CC) $(CFLAGS) parmjoin.o -o parmjoin
prepgen: prepgen.o 
	$(CC) $(CFLAGS) $(MATHS) prepgen.o  -o prepgen
respgen: respgen.o 
	$(CC) $(CFLAGS) $(MATHS) respgen.o -o respgen
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Received on Fri Mar 26 2004 - 10:53:00 PST