Hi Parul,
Your confusing is because the meaning of the 12 in the solvate
command. This value doesn't mind exactly the box size, this value is
the minimum distance between the solute and the box. I think that
there are more (and best) explanation in the manual or in the Sustiva
tutorial (Tutorial 4)
regards,
Jose Luis
Quoting parul sharma <sharmaparul7373.gmail.com>:
> 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 - 01:15:58 PST
