Re: [AMBER] antechamber

From: <>
Date: Mon, 5 Apr 2010 10:11:48 +0530 (IST)

hello sr,in response to ur suggestion,
when i gave the following command:

 antechamber -i plp.pdb -fi pdb -o plp.mol2 -fo mol2 -c bcc -s 2

i got the following error:
 Running: $AMBERHOME/exe/bondtype -i ANTECHAMBER_BOND_TYPE.AC0 -o
Warning: the assigned bond types may be wrong, please :
(1) double check the structure (the connectivity) and/or
(2) adjust atom valence penalty parameters in APS.DAT, and/or
(3) increase MAXVASTATE in define.h and recompile bondtype.C
(4) increase PSCUTOFF in define.h and recompile bondtype.C
    Be cautious, use a large value of PSCUTOFF (>10) will significantly increase
the computer time
Error: cannot run "$AMBERHOME/exe/bondtype -i ANTECHAMBER_BOND_TYPE.AC0 -o
ANTECHAMBER_BOND_TYPE.AC -f ac -j full" in judgebondtype() of antechamber.c
properly, exit

and i got the following files only:

and all are intermediate files. it seems as if the run wasn't finished properly
to get output file.

i did this without reducinh the molecule. as i was trying to reduce the molecule
by following command:
    reduce plp.pdb > plp_new.pdb
i got the following error:
   -bash: reduce: command not found
then i tried to add hyrogens using pymol and got the file and tried to give
antechamber command as above, still the same error came.moreover i cudn't
understand the errors also.

plz help me out to extract the parameters for pyridoxal phosphate molecule.
thanx in advance

> On Thu, Apr 01, 2010, wrote:
>> i tried as given in the tutorial...but the reduce command is not
>> working......such that it is only making the intermediate files only
>> (ATOMTYPE...etc.) and not making the final output files.
> We need more details: "as given the the tutorial" doesn't tell us exactly what
> you did, or what happened. The reduce command is not mandatory, so maybe you
> could skip that step. But without more information, no one can help very
> much.
> ....dac
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Received on Sun Apr 04 2010 - 22:00:02 PDT
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