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 - 09:51:54 CDT

Hi Simon,

The short (easy) answer to your question is: wet experiments are done in
salt buffers and in the cells (where biomolecules act) you also have
salt buffer.

Cheers
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
>>
>>
>> ___________________________________________________________
>> 好玩贺卡等你发，邮箱贺卡全新上线！ http://card.mail.cn.yahoo.com/
>> _______________________________________________
>> AMBER mailing list
>> AMBER_at_ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
> 

-- 
----------------------------------------------------------------------------
Dr. Vlad Cojocaru

EML Research gGmbH
Schloss-Wolfsbrunnenweg 33
69118 Heidelberg

Tel: ++49-6221-533202
Fax: ++49-6221-533298

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

http://projects.villa-bosch.de/mcm/people/cojocaru/

----------------------------------------------------------------------------
EML Research gGmbH
Amtgericht Mannheim / HRB 337446
Managing Partner: Dr. h.c. Klaus Tschira
Scientific and Managing Director: Prof. Dr.-Ing. Andreas Reuter
http://www.eml-r.org
----------------------------------------------------------------------------

_______________________________________________
AMBER mailing list
AMBER_at_ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber