AMBER Archive (2006)

Subject: AMBER: water prmtop/inpcrd problem

From: Akshay Patny (
Date: Thu Oct 05 2006 - 20:08:59 CDT

Dear Amber Users

I am trying to convert a water PDB file into the PRMTOP and
INPCRD files via LEAP. I am using Amber 8 for the same.

I used ff03 forcefield. In my initial water pdb file
“water_mod2.pdb”: there are 12 water molecules and I
have changed the residue names to WAT for leap to recognize
them as TIP3P water and the atom names are O, H1, and H2 for
each water molecule. The atom numbers are unique although do
not start from 1.

I used LEAP to load this water_mod2.pdb file and then saved
it as PRMTOP (mod2.prmtop) and INPCRD (mod2.inpcrd) as well
as PDB (mod2.pdb). Now, when I open the PRMTOP/INPCRD files
using VMD, there is an extra bond between two hydrogens for
each water molecule. Surprisingly the output PDB file from
LEAP is perfect when viewed by PDB.

Can anyone guide me why is this happening? I am attaching
files and the leap output below:

Also LEAP says following .....
(starting new molecule for chain 1)
(starting new molecule for chain 2)
(starting new molecule for chain 3)
why it starts a new molecule ... i do not have any chains.

I look forward for suggestions.

Akshay Patny

> try = loadpdb water_mod2.pdb
Loading PDB file: ./water_mod2.pdb
 (starting new molecule for chain 1)
 (starting new molecule for chain 2)
 (starting new molecule for chain 3)
  total atoms in file: 36
> saveamberparm try mod2.prmtop mod2.inpcrd
Checking Unit.
Building topology.
Building atom parameters.
Building bond parameters.
Building angle parameters.
Building proper torsion parameters.
Building improper torsion parameters.
 total 0 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:

        res total affected

        WAT 12
 (no restraints)
> savepdb try mod2.pdb
Writing pdb file: mod2.pdb

Akshay Patny

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