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
