From: Felipe Merino (felipe.merino_at_mpi-muenster.mpg.de)
Date: Sat Feb 15 2014 - 04:50:15 CST
I think I've seen these problems before as well. As far as i remember
the issue happens when you ask vmd to re-wrap the system centered on a
complex that is already separated by the wrap option of namd.
What i do is the following,
Let's say you have a dimer protein and it is only one monomer is
wrapped. Then i run
pbc unwrap -sel "protein" -all
That might be sufficient if you only want to reconstruct the complex.
then you run
pbc wrap -all -compound res -center bb -centersel "protein"
or something of the sort.
On 02/14/2014 08:25 PM, Aron Broom wrote:
> yes I've seen that happen occasionally. You need to be very careful
> in the options that you give PBC wrap.
> Did you try the line that Normal recommended?
> I would try first aligning all the frames using the RMSD trajectory
> tool (it will not be confused by periodic boundaries the way our eyes
> are, and will do everything correctly). Then use Normans line "pbc
> wrap -centersel "protein or nucleic" -center com -compound residue -all
> Does this still produce corrupted bonds?
> On Fri, Feb 14, 2014 at 2:15 PM, Kenno Vanommeslaeghe
> <kvanomme_at_rx.umaryland.edu <mailto:kvanomme_at_rx.umaryland.edu>> wrote:
> You mean, like, after wrapping atoms around the periodic boundary,
> the bonds that cross the boundary seem to span the entire box?
> On 02/14/2014 09:38 AM, Ariel Talavera Perez wrote:
> First of all. Thanks to all for the quick answers.
> So far I managed to always get the DNA and the protein dimer
> in all the
> frames. Although, the structure is completely corrupted with
> very bad
> bond distances in some frames.
> 14 09:21 PM, Norman Geist wrote:
> In VMDs console
> pbc wrap -all-compound res -center com -centersel "protein
> or nucleic"
> or similar
> Norman Geist.
> -----Ursprüngliche Nachricht-----
> Von: owner-namd-l_at_ks.uiuc.edu
> <mailto:owner-namd-l_at_ks.uiuc.edu>] Im
> Auftrag von Ariel Talavera Perez
> Gesendet: Donnerstag, 13. Februar 2014 16:57
> An: namd-l_at_ks.uiuc.edu <mailto:namd-l_at_ks.uiuc.edu>
> Betreff: namd-l: moving out of the box
> I just ran 0.5 us MD us of a protein dimer in complex
> with DNA in a
> water box. Unfortunately I did not restrain the
> neither the translation
> nor the rotation of the complex. In several frames
> part of the complex
> moved out of the water box. This makes that sometimes
> one of the
> monomers is gone from the water box, and the same
> monomer but from the
> neighbour cell appears.
> Is there anyway to fix this issue for the MD I already
> ran? I mean, how
> can I get the "right" complex in all the frames?
> Thanks a lot in advanced
> Aron Broom M.Sc
> PhD Student
> Department of Chemistry
> University of Waterloo
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