AMBER Archive (2006)

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

From: frustrated modeller (amber.jam_at_gmail.com)
Date: Wed Jul 19 2006 - 18:30:07 CDT

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
ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac -j full" in
judgebondtype() of antechamber.c properly, exit

The molecule is a modified peptide. It has no strange atom or bond types in
it but it does have nonstandard residues. What exactly does this error
mean? All the bugfixes were applied to both amber installations.

Sorry for the double post. I have attached the pdb file IPC.1.pdb
This error is from a cluster machine with i686 processors running RedHat
(not sure what exact version).

Thank you in advance for your help,

Frustrated
-
Hello.
I was trying to use antechamber from a newly installed amber9. When I
compiled amber9 all seemed fine, however at that time I only tested basic
sander. When I came to test antechamber there were errors. Bellow I will
show you what happens when I try Run.tp and Run.sustiva:

ATTENTION

The Mulliken charges were generated by divcon in amber9, you may get
different result if different QM program is applied

Total number of electrons: 58; net charge: 0

Running: $AMBERHOME/exe/divcon
forrtl: severe (174): SIGSEGV, segmentation fault occurred
Error: cannot run "$AMBERHOME/exe/divcon" of bcc() in charge.c properly,
exit
Cannot open file tp.mol2, exit
cat: tp.mol2: No such file or directory
diffing tp.mol2.save with tp.mol2
possible FAILURE: check tp.mol2.dif
==============================================================
cat: frcmod: No such file or directory
diffing frcmod.save with frcmod
possible FAILURE: check frcmod.dif
==============================================================
prmcrd: Command not found.

ATTENTION

The Mulliken charges were generated by divcon in amber9;
you may get different results if a different QM program is applied

Total number of electrons: 160; net charge: 0

Running: $AMBERHOME/exe/divcon
forrtl: severe (174): SIGSEGV, segmentation fault occurred
Error: cannot run "$AMBERHOME/exe/divcon" of bcc() in charge.c properly,
exit
Cannot open file sustiva.mol2, exit
cat: sustiva.mol2: No such file or directory
diffing sustiva.mol2.save with sustiva.mol2
possible FAILURE: check sustiva.mol2.dif
==============================================================
cat: frcmod: No such file or directory
diffing frcmod.save with frcmod
possible FAILURE: check frcmod.dif
==============================================================

I thought this may mean the build was not as successful as I had hoped. It
seems that maybe divcon is not working.

I have attatched the config.h file I used for the compilation.

What did i do wrong?

Sincerely,

Frustrated


  • application/octet-stream attachment: config.h

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