[gmx-users] Ligand moving during MD course.

[Thomas Evangelidis]

I have no comment about the ligand parameters as I am not familiar with
CHARMM ff, but as far as your protein is concerned, it doesn't sound
abnormal to see the ligand move since most crystallized prion proteins do
not have buried binding pockets.


On 30 July 2014 11:41, Raju <rajiv at kaist.ac.kr> wrote:

> Dear gmx users,
>
>
> I have simulated the crystal structure prion with its inhibitor using
> charmm27.ff force field by obtaining the inhibitor parameters from
> http://www.swissparam.ch/.
>
>
> After i ran the production for 10 ns, the output shows the inhibitor
> moving ~ 3 Angstrom from the cavity and contacting close to the cavity the
> few more different residues from protein. Even i could see the inhibitor
> moving in equilibrium state  (NPT). Moreover, i have not used any
> constrains for inhibitor.
>
>
> I have also tried another prion crystal structure with its different
> inhibitor as well docked inhibitors but in all results, the inhibitors were
> moving in different direction within 10 ns for MD production.
>
>
> I just worried whether i am using any wrong protocol or naturally it does
> happen for specific proteins?
>
>
> Your suggestion would be greatly appreciated. Thanks.
>
>
>
>
>
>
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>



-- 

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

Thomas Evangelidis

PhD student
University of Athens
Faculty of Pharmacy
Department of Pharmaceutical Chemistry
Panepistimioupoli-Zografou
157 71 Athens
GREECE

email: tevang at pharm.uoa.gr

          tevang3 at gmail.com


website: https://sites.google.com/site/thomasevangelidishomepage/