VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Jul 06 2010 - 15:39:48 CDT

Hi,
  Since you were running VMD 1.8.6, and thus a much older version of
autoionize, before we go chasing "ghost" bugs that have already been
fixed, what happens when you run either VMD 1.8.7, or one of the new
VMD 1.8.8 alpha test versions?

The alpha versions of VMD are available by following the instructions here:
  http://www.ks.uiuc.edu/Research/vmd/alpha/

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Tue, Jul 06, 2010 at 03:36:20PM -0400, Parisa Akhski wrote:
> Dear John,
>
> My DNA system has "-20" charges from (o1p) atoms and (+1) form SOD (atom
> 781) in the pdb file. In order to neutralize the system, I need to add 19
> SOD atoms using autoionize. I figured out that if I use 0.3 instead of
> 0.0001 in the command below:
>
> "autoionize -psf file.psf -pdb file.pdb -is 0.0001"
>
> The system net charge after adding ions is 8.53529961375e-007e while it
> was -18.9999991465e before adding ions. It seems that the program is
> adding 19 Na and 0 Cl ions, total 19 ions in this case to balance the
> charge. My questions are:
>
> (1) Does 8.53529961375e-007e mean 8.53529961375810^-7? If yes, is this net
> charge now in neutralization by autoionize?
>
> (2) If I use 0.28 instead of 0.3, the final net charge is -0.999999146471e
> which is very different from what produced by 0.3. Is it because of
> rounding problem as you mentioned before?
>
> Thanks,
>
> Parisa
>
> (2) If yes
>
> -----Original Message-----
> From: John Stone [mailto:johns_at_ks.uiuc.edu]
> Sent: Tue 7/6/2010 11:42 AM
> To: Parisa Akhski
> Cc: vmd-l_at_ks.uiuc.edu
> Subject: Re: vmd-l: Autoionize does not neutralize the system
>
> Hi,
> Interestingly, in reading the current version of the code, there
> are a number of checks for this kind of problem. It would seem
> that this particular case is exercising a code path that either
> isn't covered, or that you neglected to mention anything about warning
> messages that should have appeared when running the tool?
>
> It would be helpful to have the actual files that caused the problem,
> as there's clearly a case that's not being handled here.
>
> Which version of VMD are you running? (so I can get a rough
> guess which version of autoionize you're using)
>
> Cheers,
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Tue, Jul 06, 2010 at 10:16:20AM -0400, Parisa Akhski wrote:
> > Dear VMD users,
> >
> > I am using autoionize to neutralize a DNA molecule. I am using the
> command
> > below as posted on the VMD mailing list to make it only place enough
> ions
> > to neutralize the system:
> >
> > autoionize -psf file.psf -pdb file.pdb -is 0.0001
> >
> > The system net charge before adding ions is -18.9999991446e and after
> > adding ions is -0.999999144592e. Isn't that supposed to be zero after
> > adding ions? Or is it acceptable?
> >
> > Thanks in advance for your help,
> >
> > Parisa
>
> --
> NIH Resource for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> Email: johns_at_ks.uiuc.edu Phone: 217-244-3349
> WWW: http://www.ks.uiuc.edu/~johns/ Fax: 217-244-6078 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349
  WWW: http://www.ks.uiuc.edu/~johns/      Fax: 217-244-6078