AMBER Archive (2009)

Subject: [AMBER] testing RRR with antechamber

From: Alan (
Date: Mon Apr 06 2009 - 07:10:27 CDT

Hi there,

So I have this tripeptide made of NARG-ARG-CARG. The mol2 file
gRRR.mol2 is attached. When I test it with antechamber, I got:

antechamber -i gRRR.mol2 -fi mol2 -o new.mol2 -fo mol2 -nc 3

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 "/Users/alan/Programmes/amber10/bin/bondtype -j full
judgebondtype() of antechamber.c properly, exit

Similar problem happens with protonated HIS (usual HIS goes fine).

I was wondering if, before trying recommendations (2) and (3) above,
there was something else I could know from my file. It was generated
automatically by pymol and converted to mol2 via babel.

These are all part a small set of tests I am running to understand
better antechamber before applying it to my modified residues.

Many thanks in advance,


Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate
Department of Biochemistry, University of Cambridge.
80 Tennis Court Road, Cambridge CB2 1GA, UK.

  • application/octet-stream attachment: gRRR.mol2

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