Re: [AMBER] mismatch pdb files when created using ambpdb and savepdb

From: David A Case <>
Date: Mon, 8 Sep 2014 10:17:40 -0400

On Mon, Sep 08, 2014, wrote:
> Why there is mismatch in the number of atoms when created using "ambpdb"
> and "savepdb" as follow? ambpdb gives more number of water molecules.
> The pdb file created using "savepdb" gives correct number of atoms in the
> system.
> =====================
> source leaprc.ff99SB
> m = loadpdb minimized_structure.pdb
> addions m Cl- 0
> solvatebox m TIP3PBOX 14
> saveamberparm m UVI_control_solion.prmtop UVI_control_solion.inpcrd
> savepdb m UVI_solion.pdb
> quit
> ======================
> ambpdb -p UVI_control_solion.prmtop < UVI_control_solion.inpcrd > test.pdb
> ======================

This should not happen, and I have never seen it. Can you be more specific
about what you mean by "more number of water molecules"? Does the number of
atoms in test.pdb match the numbers at the top of the prmtop and inpcrd file?
Same question for UVI_solion.pdb. (To find the number of atoms, use a command
like "grep ATOM test.pdb | wc"). It might give a clue if you told us the
exact number of atoms in each of the four files.


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Received on Mon Sep 08 2014 - 07:30:02 PDT
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