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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Received on Wed Feb 11 2009 - 01:15:28 PST
