AMBER Archive (2006)

Subject: Re: AMBER: Fwd: difficulties with antechamber: tests dont even run

From: David A. Case (
Date: Tue Jul 25 2006 - 10:11:22 CDT

On Wed, Jul 19, 2006, frustrated modeller wrote:

> P.S. I forgot to mention the reason I was trying to use antechamber on the
> new installation of amber9 was due to errors I got on a different machine
> trying to run amber 8 antechamber (which is passing the tests).
> What I was trying to do and what error I got is below.
> antechamber -fi pdb -fo prepi -i IPC.1.pdb -o IPC.prep -nc 0 -at amber -c
> bcc -rf IPC.res -rn IPC -s 2
> Running: /data/people/negi/amber8/exe/bondtype -i ANTECHAMBER_BOND_TYPE.AC0
> -o ANTECHAMBER_BOND_TYPE.AC -f ac -j full
> Error: cannot run "/data/people/negi/amber8/exe/bondtype -i
> judgebondtype() of antechamber.c properly, exit

antechamber only works on *single* residues. It is getting quite confused
by the IPC.1.pdb file, which has multiple residues (and hence, several
atoms with the same name.)

> Running: $AMBERHOME/exe/divcon
> forrtl: severe (174): SIGSEGV, segmentation fault occurred

It's hard to debug this. Which version of ifort are you using (what is the
output of ifort -V)?

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