VMD-L Mailing List

From: Anton Arkhipov (anton_at_ks.uiuc.edu)
Date: Mon Sep 15 2008 - 10:15:23 CDT

> How about using the "ionize" program by Peter Freddolino?
I think that's a very good point.

Just to clarify, even if one uses the "ionize" or Autoionize plugins,
one should apply them with CG ions. By default, these plugins are
using normal ions (atoms), which would not be appropriate in a CG
model. So, one would need to prepare topology and parameter files for
CG ions, tuned for the specific CG model, and then "teach" the plugins
to employ these CG ions. This latter step is not difficult, of course.

Anton.

On 15 Sep 2008, at 10:02, L. Michel Espinoza-Fonseca wrote:

> 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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