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*
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Received on Sat Jan 26 2019 - 10:30:03 PST
