Hi
I did following in VMD
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Main console display active (Tcl8.4.1 / Tk8.4.1)
(Desktop) 26 % set sel [atomselect top all]
atomselect0
>Main< (Desktop) 27 % measure minmax $sel
{-12.9750003815 -5.4439997673 -0.989000022411} {119.277000427
106.664001465 74.4410018921}
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Thus I got following XYZ dimensions for my system:
x = 132.2520008085
y = 112.1080012323
z = 75.430001914511
Now, as the atom diameters are not calculated in VMD, so do you
recommend adding 5 A in each dimension (or may be less like 2 or 3 A)
for making a periodic box around the system
Thanks for your suggestions.
Best Regards, -Akshay Patny (Olemiss)
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Akshay Patny
PhD Candidate (5th Yr.), Computational Chemistry
Department of Medicinal Chemistry, School of Pharmacy
The University of Mississippi
805 College Hill Rd, # 9, Oxford, MS 38655
E-mail: akshay17.olemiss.edu
Phone (O): (662)-915-1286,(M): (662)-801-5496
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-----Original Message-----
From: owner-amber.scripps.edu [mailto:owner-amber.scripps.edu] On
Behalf Of David A. Case
Sent: Wednesday, January 24, 2007 9:04 AM
To: amber.scripps.edu
Subject: Re: AMBER: Defining BOX INFO during TLEAP
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
...good luck...dac
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Received on Sun Jan 28 2007 - 06:07:10 PST
