VMD-L Mailing List

From: Josh Vermaas (vermaas2_at_illinois.edu)
Date: Fri Jun 12 2015 - 09:47:24 CDT

Hmm... In principle it shoulda totally worked, but you can try things
like removing the -sel all argument? Admittedly I was going on memory,
so maybe there is something weird about all not being in quotes. I like
how it complains about an unknown option after having used it the
previous command.
-Josh

On 6/12/15 2:33 AM, Francesco Pietra wrote:
> Hi Josh:
>
> With "segname PRA" in place of your "segname A", for the same purpose,
>
> Main console display active (Tcl8.5.6 / Tk8.5.6)
> (MD_O2-out) 1% pbc wrap -sel "protein" -centersel "segname PRA"
> -center com -compound fragment
> Info) 100.0% complete (frame 4999)
> >main< (MD_O2-out) 2 % pbc wrap -sel all -centersel "protein" -center
> com -compound fragment
> error; pbcwrap: unknown option: -compound
> >Main< (Md_O2-out) 3 %
>
> Is that understandable why error?
>
> Thanks a lot
> francesco
>
> On Thu, Jun 11, 2015 at 9:31 PM, Josh Vermaas <vermaas2_at_illinois.edu
> <mailto:vermaas2_at_illinois.edu>> wrote:
>
> Here is how I do it on my own systems, which avoid the painfully
> slow unwrap process:
>
> pbc wrap -sel "protein" -centersel "segname A" -center com
> -compound fragment
> pbc wrap -sel all -centersel "protein" -center com -compound fragment
>
> The trick here is that I have one monomer (segname A) that I use
> to bring the other potentially split monomers into the same pbc
> box. The unwrap command followed by a wrap would also work, but
> you forgot the "compound fragment" argument, so the algorithm did
> what you told it to, and that is to wrap atoms around into a
> rectangle regardless of connectivity, resulting in ludicrously
> long bonds.
> -Josh Vermaas
>
>
> On 6/11/15 12:24 PM, Francesco Pietra wrote:
>> Hello:
>>
>> Following the splitting of a homotetramer into intact
>> trimer/monomer at ca 300 ns trajectory, I tried the following
>> three commands in the tk console of the remote visualization for
>> the last 24h simulation (ca 11 GB file size). I had 64GB memory
>> available (the max I could have)
>>
>> set all [atomselect top all]
>>
>> pbc unwrap -sel all (which operated very slowly on the 4999 frames)
>>
>> pbc wrap -sel all
>>
>> The latter created a box of lines of the original size. Then,
>> command "all not water" removed those pertaining to water,
>> leaving lines not amenable to any "Drawing Method". These lines
>> looked like long bonds, which were not present in the splitted
>> system.
>>
>> I used "all" as the system is also composed of ligands, some
>> firmly residing into binding pockets, some other ones traveling
>> from the surrounding medium to their binding pockets.
>>
>> The "intact" in the first line above is not entirely correct.
>> That is, the monomer is removed from the homotetramer without its
>> major ligand (the substrate to be modified by the enzyme).
>>
>> Thanks for suggestions about how to amend my faulty commands.
>>
>> francesco pietra
>
>