From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Sep 08 2016 - 16:17:43 CDT

Hi Jacob,
  I don't seem to have the email you referred to below, thanks for
resending it. We'll have a look at the modified code at the URL you
provided in the email you included below. I do have another email from
you regarding problems you saw with an unstated "new version of Tcl",
can you say more about what Tcl rev you were using when you found this?:
    When using the "pbc join connected" command, VMD is returning:
   "too many nested evaluations <infinite loop?>

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Thu, Sep 08, 2016 at 03:02:52PM -0600, Jacob Gissinger wrote:
> Hello Ajasja,
> This is a known issue after reading in certain files. I have sent a
> corrected file for 'pbc join,' but VMD has yet to utilize it or correct
> the issue.A
> Please find my original email below in case it helps with future work.
> Thanks,
> Jake
> ________________________
> Hello VMD,
> The current -bondlist option of pbcjoin is unable to
> correctlyA joinA simple chains such as the attached pdb because it does
> not actually walk the bond list as claimed in the source code. Please find
> below an updated version of pbcjoin.tcl which correctly joins large
> molecules.A
> Thanks,
> Jacob Gissinger
> Here is modified pbcjoin and example pdb. Wrap this and attempt to rejoin
> to get full effect:
> [1]https://drive.google.com/folderview?id=0B6KLDHY9t-2zfnVmbUUzS3RLdDNjQ0VzcEhNQndCN3lPVGRPa0lENmJCa1Z2cTg4Rk5XMUk&usp=sharing
> On Mon, May 30, 2016 at 2:11 AM, Ajasja LjubetiAe*
> <[2]ajasja.ljubetic_at_gmail.com> wrote:
>
> Hi!
>
> Thanks Chitrak and Norman! I tried both suggestions but still did not
> manage to wrap/join everything in one unit.
> It's funny, but just rerunning the problematic part of simulation with
> "wrapAll off" will probably be the quickest solution (in terms of my
> personal time). Ahh the joy of computer power:)
>
> Best regards,
> Ajasja
> On 30 May 2016 at 07:51, Norman Geist
> <[3]norman.geist_at_uni-greifswald.de> wrote:
>
> Hey,
>
> A
>
> If your solute is split by the periodic boundaries and are not
> connected by bonds, neither wrap a**center com a**centersel a**your
> solutea** nor pbc join can correctly work. But if therea**s a single
> atom, which can represent the center of your solute so it will
> completely fit into the periodic cell, you can use that atom for
> a**centersel
>
> A
>
> pbc wrap a**all a**compound res a**center com a**centersel a**index
> 1234a**
>
> A
>
> A
>
> Norman Geist
>
> A
>
> Von: [4]owner-vmd-l_at_ks.uiuc.edu [mailto:[5]owner-vmd-l_at_ks.uiuc.edu] Im
> Auftrag von Chitrak Gupta
> Gesendet: Freitag, 27. Mai 2016 19:48
> An: Ajasja LjubetiAe* <[6]ajasja.ljubetic_at_gmail.com>
> Cc: [7]vmd-l_at_ks.uiuc.edu
> Betreff: Re: vmd-l: Wrapping problem
>
> A
>
> Hi Ajasja,
>
> A
>
> Have you tried something like this?
>
> A
>
> pbc wrap -all -sel "water or ions" -compound res -center com
> -centersel "protein"
>
> A
>
> A
>
> This one works if:
>
> 1. All your chains are proteins
>
> 2. Only other things you have in your system apart from these chains
> come under the category "water or ions".
>
> A
>
> You could modify this based on your needs, but you get the basic
> point. Also, you could also change "-compound res" to "-compound
> fragment".
>
> A
>
> Hope this helps,
>
> Chitrak.
>
> A
>
> On Fri, May 27, 2016 at 12:10 PM, Ajasja LjubetiAe*
> <[8]ajasja.ljubetic_at_gmail.com> wrote:
>
> Dear All!
>
> I have run a simulation in NAMD using "wrapAll on". I'm simulating a
> complex of three chains.
> In one simulation (out of 14) I get large jumps, such as these
> <[9]https://gfycat.com/CapitalHollowAmmonite> (link to movie)
> <[10]https://gfycat.com/CapitalHollowAmmonite>:
>
> I have tried "pbc unwrap", "pbc wrap" and "pbc join", but Ihave yet
> to find
> the right combination of these command to correctly unwrap all three
> chains
>
> A
>
> References
>
> Visible links
> 1. https://drive.google.com/folderview?id=0B6KLDHY9t-2zfnVmbUUzS3RLdDNjQ0VzcEhNQndCN3lPVGRPa0lENmJCa1Z2cTg4Rk5XMUk&usp=sharing
> 2. mailto:ajasja.ljubetic_at_gmail.com
> 3. mailto:norman.geist_at_uni-greifswald.de
> 4. mailto:owner-vmd-l_at_ks.uiuc.edu
> 5. mailto:owner-vmd-l_at_ks.uiuc.edu
> 6. mailto:ajasja.ljubetic_at_gmail.com
> 7. mailto:vmd-l_at_ks.uiuc.edu
> 8. mailto:ajasja.ljubetic_at_gmail.com
> 9. https://gfycat.com/CapitalHollowAmmonite
> 10. https://gfycat.com/CapitalHollowAmmonite

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