AMBER: SANDER error: 'angles are not correct'

From: Fred Baba <>
Date: Wed, 13 Jun 2007 17:47:14 -0400

While attempting to run the following script to test energy
minimizations in a TIP3 box I keep getting the following error when
attempting to get a minimized .rst file in SANDER.

module load amber-9
antechamber -o ZZ1_model.mol2 -fo mol2 -i ZZ1_model.pdb -fi pdb
antechamber -i ZZ1_model.mol2 -fi mol2 -o ZZ1_model.prepin -fo prepi -c bcc -s 2
parmchk -i ZZ1_model.prepin -f prepi -o ZZ1_model.frcmod
tleap -s -f leaprc.ff99
source leaprc.gaff
ZZ1=loadpdb "ZZ1_model.pdb"
loadamberprep ZZ1_model.prepin
loadamberparams ZZ1_model.frcmod
solvateoct ZZ1 TIP3PBOX 10
saveamberparm ZZ1 ZZ1_model.prmtop ZZ1_model.inpcrd
sander -O -i -o ZZ1_model_min.out -c ZZ1_model.inpcrd -p
ZZ1_model.prmtop -r ZZ1_model_min.rst
ambpdb -p ZZ1_model.prmtop < ZZ1_model_min.rst > ZZ1_model_min.pdb

Error in Sander:

Error: ifbox=2 in prmtop but angles are not correct

I'm new to the AMBER suite and was asked to design an automated system
for running energy minimizations they run from a .pdb input file. As
I've found, the pdbs are finicky and fail more often than we'd like.
Is this a problem with the PDB file (it's a stock ligand from the
RCSB) or is there an error in my creation of the parameter files? Any
insight would be greatly appreciated.

Fred Baba

Frederick Baba
Massachusetts Institute of Technology
Class of 2010
Biological Engineering || Computer Science
Cell:(513) 886-9006
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Received on Sun Jun 17 2007 - 06:07:13 PDT
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