Re: [AMBER] how to obtain 4x4x1.1nm water

From: Jason Swails <jason.swails.gmail.com>
Date: Wed, 6 Apr 2011 23:30:14 -0700

2011/4/6 MD <ptf1242.163.com>

>
>
>
> At 2011-03-14 20:44:42ļ¼Œgromacs <ptf1242.163.com> wrote:
>
>
> Hi everyone,
>
>
> I use AMBER 9.
> Can anybody tell me how to get 4x4x1.1 box, and then fill this box with
> water (e.g. SPCBOX)?
>
> i know SolvateOct will solvate a cubic water box.
>

SolvateOct creates a truncated octahedron, not a cubic box. SolvateBox will
create a rectangular parallelpiped solvent box (sometimes a cubic water
box).

However, based on your email it seems as though what you want is not easily
doable with amber. Consider using some other software to set up your system
that specializes in that kind of system setup (for instance, packmol:
http://www.ime.unicamp.br/~martinez/packmol/).

Hope this helps,
Jason


>
>
>
> I can use command: a=copy SPC
>
> then use: solvateOct or solvateBox a SPCBOX 9
>
> but i do not know how to obtain a rectangle with water, and also need the
> density is around 1 g/cc.
>
>
>
>
> Thanks in advance!
>
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> 



-- 
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Thu Apr 07 2011 - 00:00:02 PDT
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