VMD-L Mailing List

From: Jacob Gissinger (Jacob.Gissinger_at_colorado.edu)
Date: Tue Sep 13 2016 - 14:07:02 CDT

Hello John,

I don't remember that email myself, but VMD currently returns that error
when attempting to join a molecule/crystal which is periodic via "pbc join
connected" or "pbc join connected -bondlist."

It might be best for some users if we caught that error and returned an
explanatory message.

Thanks,

Jake

On Thu, Sep 8, 2016 at 3:17 PM, John Stone <johns_at_ks.uiuc.edu> wrote:

> 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/
>