VMD-L Mailing List

From: Jacob Gissinger (Jacob.Gissinger_at_colorado.edu)
Date: Thu Sep 08 2016 - 16:02:52 CDT

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.

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 correctly join 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.

Thanks,

Jacob Gissinger

Here is modified pbcjoin and example pdb. Wrap this and attempt to rejoin
to get full effect:

https://drive.google.com/folderview?id=0B6KLDHY9t-
2zfnVmbUUzS3RLdDNjQ0VzcEhNQndCN3lPVGRPa0lENmJCa1Z2cTg4Rk5XMUk&usp=sharing

On Mon, May 30, 2016 at 2:11 AM, Ajasja Ljubetič <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 <norman.geist_at_uni-greifswald.de>
> wrote:
>
>> Hey,
>>
>>
>>
>> If your solute is split by the periodic boundaries and are not connected
>> by bonds, neither wrap –center com –centersel “your solute” nor pbc join
>> can correctly work. But if there’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 –centersel
>>
>>
>>
>> pbc wrap –all –compound res –center com –centersel „index 1234“
>>
>>
>>
>>
>>
>> Norman Geist
>>
>>
>>
>> *Von:* owner-vmd-l_at_ks.uiuc.edu [mailto:owner-vmd-l_at_ks.uiuc.edu] *Im
>> Auftrag von *Chitrak Gupta
>> *Gesendet:* Freitag, 27. Mai 2016 19:48
>> *An:* Ajasja Ljubetič <ajasja.ljubetic_at_gmail.com>
>> *Cc:* vmd-l_at_ks.uiuc.edu
>> *Betreff:* Re: vmd-l: Wrapping problem
>>
>>
>>
>> Hi Ajasja,
>>
>>
>>
>> Have you tried something like this?
>>
>>
>>
>> pbc wrap -all -sel "water or ions" -compound res -center com -centersel
>> "protein"
>>
>>
>>
>>
>>
>> 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".
>>
>>
>>
>> You could modify this based on your needs, but you get the basic point.
>> Also, you could also change "-compound res" to "-compound fragment".
>>
>>
>>
>> Hope this helps,
>>
>> Chitrak.
>>
>>
>>
>> On Fri, May 27, 2016 at 12:10 PM, Ajasja Ljubetič <
>> 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
>> <https://gfycat.com/CapitalHollowAmmonite> (link to movie)
>> <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
>>
>>
>>
>
>