AMBER Archive (2009)

Subject: Re: [AMBER] Confusion regarding box size

From: parul sharma (sharmaparul7373_at_gmail.com)
Date: Tue Feb 10 2009 - 07:29:38 CST

Thanks Jose Luis and Wei,

thanks a lot to you both, and in the manual it's also written that

"The solvent UNIT is copied and repeated in all three spatial directions to
create a box

containing the entire solute and a buffer zone defined by the buffer
argument.

If the buffer argument is a single NUMBER, then the buffer distance

is the same for the x, y, and z directions"

Does that mean the box extends itself on it's own and we do not need to give
the box size?

On Tue, Feb 10, 2009 at 3:07 PM, Wei Zhang <zgjzweig_at_gmail.com> wrote:

> 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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>>
>
>
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-- 
With Best Regards

Parul Sharma
PhD Student, Durban University of Technology,
Durban,
South Africa
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