Re: AMBER: Defining BOX INFO during TLEAP

From: David A. Case <>
Date: Wed, 24 Jan 2007 07:04:24 -0800

On Mon, Jan 22, 2007, Akshay Patny wrote:
> I have the PDB file of lipid-protein-ligand-water system which I want
> to load using TLEAP and write corresponding PRMTOP INPCRD files for
> doing simulation in AMBER 8.
> I want to do these simulations using PBC (NPT). While doing
> minimization, I got the following message >>>
> -----------------------------------------------------------------------------------------------------------------------
> | Flags: MPI
> getting new box info from bottom of inpcrd
> | peek_ewald_inpcrd: Box info not found in inpcrd
> |Largest sphere to fit in unit cell has radius = *********
> -----------------------------------------------------------------------------------------------------------------------
> Can somebody please tell me if we do not use TLEAP to solvate system
> (e.g. using solvateoct command), then what is the procedure of
> defining the BOX Info in the INPCRD and PRMTOP files?

Look at the "setBox" and "set box ..." commands in LEaP. (These are two
separate commands, and you probably want the second one.)

...good luck...dac

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Received on Sun Jan 28 2007 - 06:07:06 PST
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