AMBER Archive (2009)

Subject: Re: [AMBER] ADD SALT additional question

From: Vlad Cojocaru (Vlad.Cojocaru_at_eml-r.villa-bosch.de)
Date: Thu Jun 25 2009 - 09:55:15 CDT

Hi Simon,

Just to add to my previous email ....
Beyond the easy answer I gave you there are simulation-specific
arguments for adding only neutralizing ions to your system without
adding extra salt.

These have been discussed on this list ... if you do an archive search
you should find a lots of emails on the topic

Best
Vlad

Simon Becker wrote:
> Dear all,
>
> The question below regarding the adjustment of the system to a
> concentration of 0.1M NaCl made me thinking: why would i do this?
> I've read many publications in which certain buffer-concentrations
> where used in simulations, but nobody explained why he/she was doing
> this. Why would I place 45 na-atoms in my simulation box, far away
> from the protein (or whatever solute was investigated), far away from
> binding pockets/sites, charged sidechains, funnels or whatever. Do
> theses ions actually diffuse close to the solute, doing something
> usefull (like stabilising h2o-networks) there? Has this ever been
> observed? Guys: Why?!?
>
> Please ease my troubled mind,
> Simon
>
> ps: this is not regarding the placement of counter ions for pme
>
>
>
> -------- Original-Nachricht --------
> Betreff: Re: [AMBER] ADD SALT
> Datum: Thu, 25 Jun 2009 11:57:37 +0200
> Von: Simon Becker <simon.becker_at_uni-konstanz.de>
> Antwort an: AMBER Mailing List <amber_at_ambermd.org>
> An: AMBER Mailing List <amber_at_ambermd.org>
> Referenzen: <201339.61319.qm_at_web15704.mail.cnb.yahoo.com>
>
>
>
> hi riley,
>
> add the following two lines to your leap script:
>
> addions prot Na+ 45
> addions prot Cl- 45
>
> with 'prot' being the name you gave your system, you can also use
> 'addions2'. be aware that you have not yet changed the charge of the
> system. if you wish to use pme the net charge must be zero so adding
> more na or cl might be ne necessary.
> perform this task after solvating the system.
>
> hth
> simon
>
> Rilei Yu schrieb:
>> Dear amber users,
>>
>> I am adding salts to my system, I have calculated that 45 NaCl should
>> be added to my system to make the salt concentration reach 0.1 mol/l.
>> Can any one give me how can I perform this step? Should I perform it
>> in the xleap of others? Is there any scripts to operate this step?
>>
>> Best Regards,
>>
>> Rilei Yu
>>
>>
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> 

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e-mail:Vlad.Cojocaru[at]eml-r.villa-bosch.de

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