Hi, you may use PACKMOL (
http://www.ime.unicamp.br/~martinez/packmol/ )
for your purpose.
It is very simple and intuitive routine.
Best wishes,
Marek
Dne Mon, 14 May 2012 12:14:13 +0200 Dickson, Callum
<callum.dickson09.imperial.ac.uk> napsal/-a:
> Hi,
>
> You could try starting with a standard solvated bilayer, then heating
> the system up to 1000K or so in NVT over 1ns (or longer, depending on
> your system size). This will give you a random mix of water and lipid.
>
> Cheers,
> Callum
>
> PhD student
> Imperial College London
>
> -----Original Message-----
> From: amber-bounces.ambermd.org [mailto:amber-bounces.ambermd.org] On
> Behalf Of Lachele Foley (Lists)
> Sent: 13 May 2012 02:49
> To: AMBER Mailing List
> Subject: Re: [AMBER] Placing molecules randomly in a simulation box
>
> I'm unaware that the leaps have any built-in functions for
> randomization. But, it should be easy-ish to script. The "rand"
> command will generate random numbers (e.g., "rand -N 10" outputs 10
> random numbers... see "man rand"). Most programming languages also have
> some sort of internal randomization available. You can use those to add
> random transformations and/or translations (see manual) to your leap
> input files. The thing to make sure of is that each new random molecule
> isn't on top of another or in the middle of the protein, etc.
> Depending on your needs, you might be able to do something simple-ish
> like a a minimum COM distance check to ensure that. You might want to
> let leap add the ions and waters after the POPE's so you have less to
> worry with in the script.
>
> Of course, there might also be another utility for something like this.
>
>
> On Sat, May 12, 2012 at 2:09 PM, Massimiliano Porrini <mozz76.gmail.com>
> wrote:
>> Dear all,
>>
>> I need to randomly place ca. 200 molecules of the lipid POPE in my
>> simulation box, and then create topology and coordinates files of the
>> resulting system:
>> protein + counter ions + POPE + water
>>
>> Is there any t/xleap procedure able to randomly place POPE molecules
>> in the box (removing the potential clashing water)?
>>
>> Or I need to use another program?
>> If so, can anyone suggest me which is the best solution?
>>
>> Thanks a lot in advance.
>>
>> Best,
>>
>>
>> Dr Massimiliano Porrini
>> Institute for Condensed Matter and Complex Systems School of Physics &
>> Astronomy The University of Edinburgh James Clerk Maxwell Building The
>> King's Buildings Mayfield Road Edinburgh EH9 3JZ
>>
>> Tel +44-(0)131-650-5229
>>
>> E-mails : M.Porrini.ed.ac.uk
>> mozz76.gmail.com
>> maxp.iesl.forth.gr
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
> --
> :-) Lachele
> Lachele Foley
> CCRC/UGA
> Athens, GA USA
>
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Received on Mon May 14 2012 - 05:00:06 PDT
