VMD-L Mailing List

From: Suresh (suresh.gorle_at_research.iiit.ac.in)
Date: Thu Oct 10 2013 - 23:36:02 CDT

Hi,

the reason might be with the lack of topology/parameters for your ligand. Charmm-gui will try to assign the topology/parameters based on the pre-defined residues and leave space for the molecule for which the parameters are not defined. There is an option to give topology /parameters for non-standard molecule. The possible solution is get the ligand parameters and topology using https://www.paramchem.org/ server. Careful with the penalties of the parameters generated by the server.

Hope this helps

Suresh

----- Original Message -----
From: "Ramin Ekhteiari" <ramin_ekh_at_yahoo.com>
To: "vmd-l" <vmd-l_at_ks.uiuc.edu>
Sent: Thursday, October 10, 2013 11:08:11 PM
Subject: vmd-l: embed a protein that includes a ligand into the membrane

Hi,

I am trying to embed protein that includes a ligand into the membrane bilayer via charmm-gui server.. but during generating, it removes my ligand.
would you please advise me on how to solve it?
would be grateful for any help.

Cheers,
Ramin