I've seen that happen also, when I added charges FIRST, before solvating.
If this is the case, then simply solvate FIRST, then add the ions.
This will also make your water box much smaller, since you are replacing
waters with ions and the overall dimensions of the just the protein is much
smaller than the overall dimensions of the protein with ions.
Hope this helps!
Dean
> From: InSuk Joung <i.joung.gmail.com>
> Reply-To: AMBER Mailing List <amber.ambermd.org>
> Date: Tue, 20 Apr 2010 09:44:24 -0500
> To: AMBER Mailing List <amber.ambermd.org>
> Subject: Re: [AMBER] Setup of defined salt concentrations
>
> If you think the ions are not distributed uniformly, you can use the ptraj
> command, 'randomizeions'. Please refer to AmberTools manual.
> By the way, why do you think the distribution is dependent on your system?
> I believe Leap should not give different results depending on systems.
>
> On Tue, Apr 20, 2010 at 9:16 AM, Anselm Horn <
> Anselm.Horn.biochem.uni-erlangen.de> wrote:
>
>> Dear all,
>>
>> (I apologize if this question has been asked and answered before)
>>
>> is there a canonical way in the Amber community to add ions (e.g. Na+
>> and Cl-) not for charge neutralization of the protein system, but to
>> create a given (e.g. physiological) salt concentration in the solution?
>>
>> In the Amber mail archives I found a perl script from Thomas Cheatham
>> that computes the number of necessary molecules from a given volume.
>>
>> Of course, these ions can then be added with leap.
>> However, when I tried it once for a single system, all ions appeared
>> rather crowded and were not distributed in an approximately uniform way
>> in the solvent box; this could have been an outcome of my system, of
>> course.
>>
>> So my question is: How do other people deal with this?
>>
>> Thanks in advance for your advice.
>>
>> Regards,
>>
>> Anselm
>>
>> Bioinformatik
>> Friedrich-Alexander-Universität Erlangen-Nürnberg
>> Germany
>>
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
>
> --
> Best,
> InSuk Joung
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Received on Tue Apr 20 2010 - 09:30:03 PDT
