VMD-L Mailing List
From: Anton Arkhipov (anton_at_ks.uiuc.edu)
Date: Mon Sep 15 2008 - 09:10:04 CDT
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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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- Next message: Anirban Ghosh: "How to ionize a Shape Based CG Model?"
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- In reply to: Anirban Ghosh: "How to ionize a Shape Based CG Model?"
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- Reply: L. Michel Espinoza-Fonseca: "Re: How to ionize a Shape Based CG Model?"
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