VMD-L Mailing List

From: Josh Vermaas (vermaas2_at_illinois.edu)
Date: Thu Jun 11 2015 - 14:31:39 CDT

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