AMBER: Problem about prepare the model when running antechamber

From: Liang, Lei <>
Date: Mon, 04 Jun 2007 15:04:36 -0500

Dear Amber users

I ran antechamber to parameterize my molecule consists of 1125 atoms.

It is a collagen model which consists of 3 molecules.

Next was my antechamber command:

$AMBERHOME/exe/antechamber -i 7-2-het_starting.pdb -fi pdb -o
7-2-het_starting.prepin -fo prepi -c bcc -s 2

The atom number exceeds the MAXATOM, reallocate memory
Info: the bond number exceeds MAXBOND, reallocate memory automatically
Running: /usr/local/amber9/exe/bondtype -i ANTECHAMBER_BOND_TYPE.AC0 -o

Info: the atom number exceeds the MAXATOM, reallocate memory automatically
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 "/usr/local/amber9/exe/bondtype -i
judgebondtype() of antechamber.c properly, exit


Also, I tried to load the pdb file to LEaP, it gives me the
information as following:


!FATAL ERROR----------------------------------------
!FATAL: In file [atom.c], line 444
!FATAL: Message: bondAtomProblem found


Here I send the pdb file as the attachment. Could anyone please to give
me some help? Can the antechamber parameterize the unusually long
organic molecule like mine?


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Received on Wed Jun 06 2007 - 06:07:21 PDT
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