AMBER Archive (2009)

Subject: Re: [AMBER] Confusion regarding box size

From: Wei Zhang (zgjzweig_at_gmail.com)
Date: Tue Feb 10 2009 - 07:07:38 CST

Hi Parul,

    The 12 A is not box size, but buffer size, the following is
taken from manual

"

The buffer
argument defines the distance, in angstroms, between
the wall of the box and the closest ATOM in the solute.
"

Sincerely,

Wei

On Feb 10, 2009, at 1:20 AM, parul sharma wrote:

> Dear all,
>
> I created tip3p box using leaprc and it looks like
>
> source leaprc.ff96
> loadAmberParams frcmod.WAT
> nmb = sequence {NGLY ASN LEU TRP ALA THR GLY HIS PHE MET NHE}
> solvateBox nmb TIP3PBOX 12
> addIons nmb Na+ 15 Cl- 15
> saveamberparm nmb nmb.prmtop nmb.prmcrd
> quit
>
>
> when i view the leap.log file it looks like
>
> Total vdw box size: 64.737 52.178 36.583
> angstroms.
> Volume: 123570.855 A^3
> Total mass 55379.498 amu, Density 0.744 g/cc
> Added 3011 residues.
>> addIons nmb Na+ 15 Cl- 15
> Adding 30 counter ions to "nmb" using 1A grid
> Total solute charge: 1.00 Max atom radius: 2.00
> Grid extends from solute vdw + 1.87 to 7.87
> Box:
> enclosing: -25.21 -19.20 -11.32 25.37 19.18 10.94
> sized: 38.79 44.80 52.68
> edge: 64.00
>
>
> My confusion is reagrding the box size, in leaprc by "12" i mean
> that i
> genrated a cubic box of dimensions 12 Angstroms, but in leap.log
> file the
> box size as you can see is of dimensions 64.737 52.178 36.583
> angstroms,
> so what was this 12 i used in the leaprc?
>
> My assumption is that by saying solvateBox nmb TIP3PBOX 12 in the
> leaprc a
> UNIT box of 12 Angstrom is genearated and this UNIT box of 12
> repeats to
> form a bigger box according to the peptide size, but i am not sure of
> anything. Please help
>
> --
> With Best Regards
>
> Parul Sharma
> PhD Student, Durban University of Technology,
> Durban,
> South Africa
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> AMBER_at_ambermd.org
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