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.uni-konstanz.de>
Antwort an: AMBER Mailing List <amber.ambermd.org>
An: AMBER Mailing List <amber.ambermd.org>
Referenzen: <201339.61319.qm.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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--
Simon Becker
Dept. of Biology
Molecular Bioinformatics
Box M647
Universitaet Konstanz
D-78457 Konstanz
mail: simon.becker.uni-konstanz.de
Tel: 0049 7531 882900, Fax: 3183
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--
Simon Becker
Dept. of Biology
Molecular Bioinformatics
Box M647
Universitaet Konstanz
D-78457 Konstanz
mail: simon.becker.uni-konstanz.de
Tel: 0049 7531 882900, Fax: 3183
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Received on Mon Jul 06 2009 - 11:14:42 PDT
