AMBER Archive (2009)

Subject: Re: [AMBER] Unit 8 Error on OPEN: prmtop

From: Peter Gannett (
Date: Sun May 24 2009 - 12:46:47 CDT

Check and make sure the prmtop file is in the directory you started sander from. It looks like leap wrote the file but you might have a look, anyway, and make sure there is something in there.

>>> On 5/24/2009 at 1:27 PM, in message <>, "Workalemhu Berhanu" <> wrote:
Dear all

I am new to the amber software and I am using amber9. When Load my pdb file in xleap it went well and created the topology and Cartesian coordinate. But when in used the top and crd file to run minimization of the created structure in sander it is not working and it says Unit 8 Error on OPEN: prmtop. Could please help in figuring out what went wrong? Thank you
> model = loadpdb "Mggvvia.pdb"
Loading PDB file: ./Mggvvia.pdb
  total atoms in file: 36
  Leap added 42 missing atoms according to residue templates:
       42 H / lone pairs
> saveamberparm model Mggvvia_vac.prmtop Mggvvia_vac.inpcrd
Checking Unit.
Building topology.
Building atom parameters.
Building bond parameters.
Building angle parameters.
Building proper torsion parameters.
Building improper torsion parameters.
total 11 improper torsions applied
Building H-Bond parameters.
Not Marking per-residue atom chain types.
Marking per-residue atom chain types.
  (Residues lacking connect0/connect1 -
   these don't have chain types marked:

restotal affected

(no restraints)
$AMBERHOME/exe/sander -O -i -o Mggvvia_gb_init_min.out -c Mggvvia_vac.prmtop -r Mggvvia_gb_init_min.rst

  Unit 8 Error on OPEN: prmtop

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