[gmx-users] PROTEIN FOLDING
drrahulsuresh at gmail.com
Tue Dec 19 08:23:03 CET 2017
On Tue, 19 Dec 2017 at 12:36 PM, Neha Gupta <nehaphysics17 at gmail.com> wrote:
> Hi gromacs users,
> After MD simulation of protein-ligand complex for 5ns, can we view protein
You can use various supporting tools from R language to debug your
trajectory but most third party software support NAMD and charmm format.
You can use VMD to convert the trajectory to dcd and use R language based
packages to read your trajectory
> How to do it?
> I want to ascertain if there is any conformation change in protein where
> the ligand binds. Is it possible?
> We observe hydrogen bonds through molecular docking. Hence, I want to make
> observation through MD simulation which is not obtained through docking.
> Can someone help me regarding this?
> Thank you very much in advance.
> Gromacs Users mailing list
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> * 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.
More information about the gromacs.org_gmx-users