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.
Script:
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
quit
sander -O -i test.in -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.
Thanks,
Fred Baba
--
Frederick Baba
Massachusetts Institute of Technology
Class of 2010
Biological Engineering || Computer Science
Email: fredbaba.mit.edu, fred.baba.gmail.com
Cell:(513) 886-9006
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Received on Sun Jun 17 2007 - 06:07:13 PDT
