[gmx-users] pbc whole

[Justin A. Lemkul]

Carla Jamous wrote:
> Hi Justin,
> Thank you for your answer but I'm still not getting my ligand to stay in 
> the box.
> 
> I tried the following(after taking a look at the mailing list archive):
> 
> trjconv -s a.tpr -f b.xtc -o c.xtc -center -ur compact -pbc mol 
> (centering on "Protein")
> trjconv -s d.tpr -f c.xtc -o f.xtc -fit rot+trans
> 
> So please do you have another advise to give me?
> 

If that's not working, then I wonder if your ligand is still actually bound to 
your protein :)  The above sequence always works for me, as long as there 
actually is a complex.  You can also try -pbc cluster, but I know that algorithm 
can hang.

-Justin

> Thanks
> Carla
> 
> On Mon, Feb 15, 2010 at 4:32 PM, Justin A. Lemkul <jalemkul at vt.edu 
> <mailto:jalemkul at vt.edu>> wrote:
> 
> 
> 
>     Carla Jamous wrote:
> 
>         Hi everyone,
>         I'm using this command to extract my protein and my ligand from
>         the trajectory.
> 
>         trjconv -f prot_md60ns.xtc -s prot_md50.tpr -fit rot+trans -pbc
>         whole -n prot_wat.ndx -o prot_ligand_60ns.xtc < grps >& outtrj
> 
>         Before, I had a problem with residues of my protein showing at
>         the other end of the box, when I display my .xtc with VMD.
>         the "-pbc whole" fixed it.
> 
>         However, now I have another issue: my ligand is at the other end
>         of the box. So please can anyone tell me what can I do to fix
>         that and get a reasonable RMSD value?
> 
> 
>     You may need several more iterations of trjconv (one rarely does the
>     trick), employing -pbc nojump, -pbc cluster, and/or -center.  For
>     protein-ligand complexes, I have often found that the combination of:
> 
>     trjconv -pbc mol -ur compact -center
> 
>     (centering on "Protein")
> 
>     does the trick.  And it makes molecules whole, as well :)  I think
>     there are also some breakdowns (documented somewhere in the list
>     archive) when applying -fit and -pbc in the same step.  I believe it
>     is recommended to fix PBC first, then applying any sort of fitting
>     in a separate, subsequent step.
> 
>     -Justin
> 
>         Thank you
>         Carla
> 
> 
>     -- 
>     ========================================
> 
>     Justin A. Lemkul
>     Ph.D. Candidate
>     ICTAS Doctoral Scholar
>     MILES-IGERT Trainee
>     Department of Biochemistry
>     Virginia Tech
>     Blacksburg, VA
>     jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
>     http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 
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> 

-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================