Thanks anyway.
-Fred
On 6/13/07, Fred Baba <fred.baba.gmail.com> wrote:
> 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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>
--
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 - 06:07:24 PDT
