AMBER Archive (2009)

Subject: [AMBER] Confusion regarding box size

From: parul sharma (sharmaparul7373_at_gmail.com)
Date: Tue Feb 10 2009 - 01:20:01 CST

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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