Hi Harmeet,

The specific error you are getting means that LeAP doe not recognize any of the atoms in the NCT residue. In other words NCT is not in it's database. Before you can set up your system with LeAP you'll need to generate force field parameter files for NCT using Antechamber. My suggestion is to work through tutorial B4 on Amber's webpage (http://ambermd.org/tutorials/basic/tutorial4b/) and then read the section of the manual on Antechamber. That should be enough to get you started, and if you run into trouble feel free to ask more questions. 

However, make sure you do a literature search: my guess is someone has already simulated a nicotine containing system in Amber, and might be willing to share the parameter files with you.

Finally, for Amber related questions, I recommend using the Amber mailing list directly: http://lists.ambermd.org/mailman/listinfo/amber.

Pawel

https://sunxiaoquan.wordpress.com/2015/02/03/the-best-tutorial-of-parametrization-for-amber-by-sergio-ruiz/

Combine the tutorial of AMBER (http://ambermd.org/tutorials/basic/tutorial4b/) and the above link, you may solve most problems about self fitting force field.

Thanks a lot to both of you. I have done that  Pawel and got same reply from Amber archive. I will try using Antechamber and will surely get back if required.

Yeah, I saw your post just after I answered it here:)

I have tried all source of information and all types of parameterization protocols but not be able to make parameters of my ligands. Kindly help me out in making parameters for small organic molecule

Hello Harmeet and Ravindra Singh,

I am completely agree with Dr. Pawel A Janowski. To start a MD simulation run for a protein-ligand system its utmost important to prepare your ligand for MD simulation by generating various parameter files. For this Antechamber (one of the inbuilt program of AMBER package) and Tleap program can be utilized. The tutorial suggest by Dr. Pawal is the right choice to understand about Antechamber and Tleap program.