Re: AMBER: size of pdb

From: David A. Case <>
Date: Sat, 12 Jul 2008 07:45:51 -0700

On Fri, Jul 11, 2008, Boutheina Kerkeni wrote:
> I have a pdb fie containing 12180 atoms and 813 residues.
> When I load it to leap and add waters/
> solvateoct pdb TIP3PBOX 9.
> The newly solvated file contains more than 99999 atoms....
> and leap replaces the number of atoms beyond 99999 by stars.

This is a limitation of the PDB format. I think ambpdb "solves" this is in a
different way than LEaP does, so you might try that.

> I suppose the max number of atoms should not exceed 99999.

No, this is not true. However, if you are new to Amber, I would recommend
making sure that you are comfortable with smaller simulations (say 50-100
residues) before starting on such a big system.

...good luck...dac

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Received on Sun Jul 13 2008 - 06:08:05 PDT
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