Yes, i search the maillist. Many people suggest packmol.
I need 4x4x1.1 and the density should also be at around 1g/cc.
So i think it is not easy for AMBER to handle. But if i use other software, how can i let AMBER know the .pdb?
I get a .pdb from Gromacs, the .pdb is 4x4x1.1 water and the density is OK (about 1g/cc), but when i load this .pdb to leap, it said 'created a new atom named: HW1 within residue: .R<SOL 226>'
i need to modify ...
At 2011-04-07 14:30:14£¬"Jason Swails" <jason.swails.gmail.com> wrote:
>2011/4/6 MD <ptf1242.163.com>
>
>>
>>
>>
>> At 2011-03-14 20:44:42£¬gromacs <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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>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
>
>--
>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 - 00:30:02 PDT
