Hi,
The issue is that autoimage considers the first molecule (in this case
probably only one monomer) of the system to center and image. How are you
measuring the distance anyway? Cpptraj should correct considering images by
default if I'm not wrong. You could try either centering and imaging things
yourself, or check if unwrapping your trajectory does the trick. As
Stephane said, check the manual for commands regarding this. An idea could
be
center :monomer_resids
image
center :dimer_resids
image
center :trimer_resids
...
and so on until you cover the pentamer, and then trajout. If your box is
too tight might not work, but might be worth a try.
Hope it helps.
Cheers,
El sáb., 26 ene. 2019 a las 19:25, Rajarshi Roy (<phd1701171011.iiti.ac.in>)
escribió:
> I am already using autoimage command in all my cases. Do I need to do
> anything else?
>
> On Sat, Jan 26, 2019 at 6:08 PM ABEL Stephane <Stephane.ABEL.cea.fr>
> wrote:
>
> > Hi,
> >
> > This seems caused by the PBC, you have to center your protein-ligand in
> > the box before to compute the properties you want (for instance distance
> > RMSD, distances, etc.) See the Amber manual for details
> >
> > Stéphane
> >
> >
> > ________________________________________
> > De : Rajarshi Roy [phd1701171011.iiti.ac.in]
> > Envoyé : samedi 26 janvier 2019 08:11
> > À : AMBER Mailing List
> > Objet : [AMBER] Unusual separation between protein and ligand
> >
> > Dear AMBER users and developers,
> > I am performing a md simulation of a pentamer protein with ligands. Each
> > monomer is having a ligand. But in case of two monomer among five,
> ligands
> > are separated up to 50 angstroms and again came back to its original
> > binding position. However, this kind of separation is not showing if I
> run
> > a movie of all this trajectory files or creating pdb of all this frames
> > using ambpdb command. Only, if I use trajin and trajout command to
> extract
> > that frame it is showing. I think there must be some error in simulation
> or
> > visualization or something else. Another unusual thing is found from the
> > pdb that the same ligand is showing in completely opposite site of the
> > protein. I am not able to make any sense from this trajectory . I also
> > attached the plot of the distance between ligand and the protein. Red one
> > is showing the unusual separation where the other ligand (green) stays in
> > the neighborhood of the protein.
> > Please suggest what will be possible explanation regarding this.
> > Thank you in advance.
> > --
> > *with regards*
> >
> > *Rajarshi Roy*
> >
> >
> > *PhD Research Scholar*
> >
> > *Biosciences and Biomedical Engineering*
> >
> > *Indian Institute of Technology, Indore*
> > *India*
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
> --
> *with regards*
>
> *Rajarshi Roy*
>
>
> *PhD Research Scholar*
>
> *Biosciences and Biomedical Engineering*
>
> *Indian Institute of Technology, Indore*
> *India*
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Stephan Schott Verdugo
Biochemist
Heinrich-Heine-Universitaet Duesseldorf
Institut fuer Pharm. und Med. Chemie
Universitaetsstr. 1
40225 Duesseldorf
Germany
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Received on Sat Jan 26 2019 - 12:00:03 PST
