AMBER Archive (2009)

Subject: [AMBER] Thanks Simon and Vlad!

From: Rilei Yu (yulaomao1983_at_yahoo.com.cn)
Date: Thu Jun 25 2009 - 18:32:35 CDT

Thanks Simon and Vald,
 
Your dicussion really benefit me greatly! In fact, when I add some salt to my system, I just want it more approach the cell environment. It is true that the effect of the salts may be neglected in the MD.
 
Regards,

Rilei Yu

--- 09年6月25日，周四, Vlad Cojocaru <Vlad.Cojocaru_at_eml-r.villa-bosch.de> 写道：

发件人: Vlad Cojocaru <Vlad.Cojocaru_at_eml-r.villa-bosch.de>
主题: Re: [AMBER] ADD SALT additional question
收件人: "AMBER Mailing List" <amber_at_ambermd.org>
日期: 2009年6月25日,周四,下午10:51

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
>>
>>
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>
>

-- ----------------------------------------------------------------------------
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/

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