You need to create your own system parameters because a drug molecule is not a standard molecule like protein/DNA. You did not mention the software you are using for this purpose. If you are using gromacs, this link will be helpful. http://www.mdtutorials.com/gmx/free_energy/index.html

no, i'm working with namd software.

I have used GROMACS for FEP calculations.

I have used GROMACS. please visit following link.

http://www.mdtutorials.com/gmx/free_energy/index.html

Hello,

a NAMD tutorial for the calculation of binding free energy for a ligand is available at the following link : https://www.ks.uiuc.edu/Training/Tutorials/#fep

The ligand parameters depends of the forcefield that you plan to use.

If you use CHARMM forcefield, you should use Cgenff server (https://cgenff.paramchem.org/commonFiles/newsEvents.php).

If you prefer AMBER forcefiel, you should use ANTECHAMBER and GAFF (http://ambermd.org/antechamber/).

Cheers,

Gautier.

i have read this tutorial mr.Gautier, but there isn't complete description to creating input file such as pdb file (zero.fep). do you understand what i'm say?

Do you mean how to generate the topology file for your ligand ?

If it is your question, you have to upload your molecule (in mol2 format with all the hydrogen atoms) and the Cgenff server creates the topology file.

You have to modify manually it for alchemical transformation (what atoms will be replaced).

Then, you follow the instructions in the tutorial.

i think you made a mistake,

i have used this method several times but there isn't any topology information, doesn't it?

the output of this method is parameter file, right?!

Yes, you're right.

Sorry, I did a word confusion in my previous post : Cgenff server outputs parameters files.