Hi,
"addIons" is usually used for neutralizing a protein, if you want to have
a box with a positive net salt concentration, use "addions2 mol Na+ N
(number of Ion that you need)"
best
On Wed, Jun 13, 2018 at 3:11 PM, Kasprzak, Wojciech (NIH/NCI) [C] <
wojciech.kasprzak.nih.gov> wrote:
> Dear Amber Users,
>
> I tried 3 LEaP script variants in order to create a solvent box with a
> positive net salt concentration.
> The common commands are:
>
> mol = loadpdb RNA.pdb
> addIons mol Na+ 0
> solvateBox mol TIP3PBOX 12.0 0.8
>
> At this stage water box with RNA and neutralizing ions inside it is
> produced.
>
> Commands:
> addIonsRand Na+ 100
> addIonsRand Cl- 100
> yield the above system with additional ions inside the water box. There
> appear to be areas
> (sub-volumes) of mostly Na+ or Cl- ions, but overall it's fairly well
> "stirred."
>
> However, using addIons instead of AddIonsRand places quite a few ions well
> outside
> the box, some at distances close to 30A from the RNA. The same
> equilibration protocol
> executed with both systems, but I am not sure how were the ions outside
> the box
> treated in a PME/PBC mix of heating , minimizations and md steps. Could
> someone
> clarify what happens to a system created with all addIons commands.
>
> Thank you in advance, Voytek
>
> Wojciech (Voytek) K. Kasprzak (Contractor)
> Bioinformatics Analyst
> Basic Science Program
> Frederick National Laboratory for Cancer Research
> Leidos Biomedical Research, Inc.
> Post Office Box B
> Frederick, Maryland 21702
> Phone: 301-846-5537
> kasprzaw.mail.nih.gov
> http://binkley2.ncifcrf.gov/users/kasprzak
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Parviz Seifpanahi
Ph.D. Candidate
Department of Physics
Virginia Tech, Blacksburg, Va 24061
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Jun 13 2018 - 12:30:02 PDT
