AMBER Archive (2009)

Subject: [AMBER] antechamber cation failure

From: Rausch, Felix (
Date: Wed Jan 14 2009 - 07:32:04 CST

 <<TCA.mol2>> <<TCA.pdb>>
Dear all,

I try to set up some QM/MM calculations for a protein using AMBER10.
Therefore, I have to prepare the ligand (terpinyl cation) with antechamber.
I tried to do so by using the following command:

antechamber -i TCA.pdb -fi pdb -o TCA.prepin -fo prepi -c gas -s 2 -nc 1

But instead of the prepin file I get the following error message:

Running: /soft/amber10/bin/bondtype -j full -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 PSCUTOFF in define.h and recompile bondtype.c
    Be cautious, use a large value of PSCUTOFF (>100) will significantly
increase the computation time

Error: cannot run "/soft/amber10/bin/bondtype -j full -i
judgebondtype() of antechamber.c properly, exit

When starting from a mol2 file the resulting message is the same. I checked
the structures in Sybyl and for me, they seem to be ok. Both input files are
attached to this message.

Since the error occurs already during the assignment of the bond types,
changing the charge method (gas, bcc, resp) doesn't have an effect.

I would be very appreciate for any suggestions.

Felix Rausch

  • application/octet-stream attachment: TCA.mol2

  • application/octet-stream attachment: TCA.pdb

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