VMD-L Mailing List

From: Nikhil Maroli (scinikhil_at_gmail.com)
Date: Thu Oct 22 2015 - 12:59:02 CDT

docking + MD is not such a common approach

Dear sir,
i wanted to run MD for only one conformation,so i have pdb of protein and
ligand i created psf for both,sorry for the mistake in the question,
so if i merge both in one file i cant conform that it will be in correct
position that is docked position.
instead of that if i make both in one pdb and creating psf will work ?
it is something like enzyme ligand Molecular dynamics.

thanks in advance

On Thu, Oct 22, 2015 at 8:09 PM, Mayne, Christopher G <cmayne2_at_illinois.edu>
wrote:

> Nikhil,
>
> Please continue to cc VMD-L on email so that others can learn from the
> conversation.
>
> There are many ways to construct systems for simulation. In this case you
> can construct a single PSF file for the receptor; however, if your docking
> allows for any flexibility in the protein, you’ll need separate PDB files
> for each conformation. Presumably all of your docked ligands have unique
> structures, which means that you’ll need a PSF file specific to the ligand
> and a PDB file specific to each pose. A much larger problem is making sure
> that you have parameters required for perform the simulations, as this is
> very often non-trivial for small molecules. For this reason, among others,
> docking + MD is not such a common approach, and we do not have any
> tutorials covering it.
>
> Regards,
> Christopher Mayne
>
> On Oct 22, 2015, at 2:40 AM, Nikhil Maroli <scinikhil_at_gmail.com> wrote:
>
> Thank you Christopher,
> i have another doubt ,i wanted to do MD after docking so should i make one
> pdb and psf for receptor+ligand or there is any other ways ?
> is there any tutorial or information how to do MD after docking?
> thanks in advance
>
>
> 

-- 
Ragards,
Nikhil Maroli