I took a look at your molecule, the problem is caused by some atom
names. The antechamber recognizes element and/or atom types only based
on atom names for the pdb format. Molecular names in the following lines
cannot be recognized by antechamber. Please modify the atom names and
run antechamber again.
ATOM 8 AG IPC 3 -7.780 -5.252 -26.581 0.00 0.00 iAb5 C
ATOM 9 AD1 IPC 3 -6.605 -5.206 -25.820 0.00 0.00 iAb5 C
ATOM 11 AE1 IPC 3 -6.593 -4.578 -24.571 0.00 0.00 iAb5 C
ATOM 13 AZ IPC 3 -7.745 -3.950 -24.093 0.00 0.00 iAb5 C
...........
Good luck
Junmei
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
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Wed Jul 26 2006 - 06:07:14 PDT
