Thank you all for the hints.
I followed Lachele's suggestion though and
I am almost done with writing my own fortran code.
It does not work yet, but I will make it :-)
ATB,
2012/5/14 Marek Maly <marek.maly.ujep.cz>:
> 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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>
>
> --
> Tato zpráva byla vytvořena převratným poštovním klientem Opery:
> http://www.opera.com/mail/
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--
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
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Received on Mon May 14 2012 - 05:00:06 PDT
