VMD-L Mailing List

From: Mayne, Christopher G (cmayne2_at_illinois.edu)
Date: Thu Oct 22 2015 - 09:39:02 CDT

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<mailto: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