VMD-L Mailing List

From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Fri Jun 12 2015 - 02:33:33 CDT

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> 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
>
>
>