[gmx-users] pbc whole

[Carla Jamous]

Hi,
Actually, the ligand I'm using is an ATP molecule, and from the beginning,
ATP is not bound to my protein by a chemical bond. It is just crystallized
with my protein.
I checked with genconf & now I'm certain that my ATP molecule is still with
the protein, but why trjconv doesn't work & why I can't get my ATP molecule
to stay within the box I'm looking at?

Thanks,
Carla

On Tue, Feb 16, 2010 at 5:44 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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
>
> ========================================
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