AMBER Archive (2004)

Subject: Re: AMBER: How to compile antechamber?

From: Julien Michel (j.michel_at_soton.ac.uk)
Date: Fri Mar 26 2004 - 04:35:11 CST

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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