VMD-L Mailing List

From: L. Michel Espinoza-Fonseca (mef_at_ddt.biochem.umn.edu)
Date: Mon Sep 15 2008 - 10:02:27 CDT

How about using the "ionize" program by Peter Freddolino?

http://www.ks.uiuc.edu/Development/MDTools/ionize/

I was using it to ionize very big systems, but I think it'll be also
useful for what you need to do. The big advantage of the program is
that it can add ions without replacing them by waters.

Peter, please correct me if I'm wrong :)

Cheers,
Michel

On Mon, Sep 15, 2008 at 4:10 PM, Anton Arkhipov <anton_at_ks.uiuc.edu> wrote:
> Hi Anirban,
> Even though you are asking the VMD list, it's me again answering to you :-).
>
> I have built a CG model (of 45 CG beads) of my protein and the net charge of
> the CG model is -2e. I want to simulate it in implicit solvent condition, so
> how to neutralize it?
>
> One thing is that you may not need to neutralize your protein for these CG
> simulations. Since you will not use PME, NAMD will run even if the total
> charge of the system is not 0.
> However, it might be a good idea to neutralize the charge anyway. To do
> that, just add ions manually. In your case, it probably should be just one
> ion, with the charge +2e and mass equal to the average mass of you protein
> CG beads. Create a PDB file with this single ion CG bead - choose its
> coordinates as you like. Also create a topology and parameter file for this
> ions. Please see examples of the topology and parameter files that you have
> created already for your protein CG model. You will just need to specify the
> charge and mass of the ion in the topology file. In the parameter file,
> provide non-bonded interaction parameters, just according to your liking.
> Then update the psfgen script I've sent to you earlier - add the PDB and
> topology for the ion there, and build your system; now you will have the ion
> added to your protein.
> Check NAMD tutorial for the details about PDB, PSF, topology and parameter
> files!
>
> I tried to add ions to the all atom PDB without solvating it (as I want to
> run in implicit condition), through "Add Ion" plugin of VMD, but it is
> giving some error:
>
> This plugin works on solvated systems; it replaces water molecules by ions.
> Since you don't have any water molecules in your system, the plugin failed.
> Just add ion(s) manually, as I suggested above.
> Anton.
>
>
> On 15 Sep 2008, at 08:09, Anirban Ghosh wrote:
>
> Hi ALL,
>
> I have built a CG model (of 45 CG beads) of my protein and the net charge of
> the CG model is -2e. I want to simulate it in implicit solvent condition, so
> how to neutralize it? I tried to add ions to the all atom PDB without
> solvating it (as I want to run in implicit condition), through "Add Ion"
> plugin of VMD, but it is giving some error:
>
> while executing
> "exit"
> (procedure "autoionize_core" line 127)
> invoked from within
> "autoionize_core -psf /home/anirban/Desktop/TRY_2/CG_TNF.psf -pdb
> /home/anirban/Desktop/TRY_2/CG_TNF.pdb -o ionized -seg ION -is 0.5 -from 5
> -between 5"
> ("eval" body line 1)
> invoked from within
> "eval autoionize_core $args "
> invoked from within
> "if $errflag { error $errMsg $savedInfo $savedCode }"
> (procedure "autoionize" line 8)
> invoked from within
> "autoionize -psf /home/anirban/Desktop/TRY_2/CG_TNF.psf -pdb
> /home/anirban/Desktop/TRY_2/CG_TNF.pdb -o ionized -seg ION -is 0.5 -from 5
> -between 5"
> ("eval" body line 1)
> invoked from within
> "eval autoionize $command_line"
> (procedure "::Autoi::run_autoi" line 70)
> invoked from within
> "::Autoi::run_autoi"
> invoked from within
> ".autoigui.autoi invoke"
> ("uplevel" body line 1)
> invoked from within
> "uplevel #0 [list $w invoke]"
> (procedure "tk::ButtonUp" line 22)
> invoked from within
> "tk::ButtonUp .autoigui.autoi
> "
> (command bound to event)
>
> How should I neutralise my CG model?
>
> Thanks,
>
>
> Anirban Ghosh
> M.Tech Bioinformatics
> University of Hyderabad
>
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