AMBER Archive (2006)

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

From: Junmei Wang (jwang_at_encysive.com)
Date: Tue Jul 25 2006 - 18:00:04 CDT

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
        
        
        
        
        

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