Dear Ben,

If you have got the desired pose from docking result and you have a target by hand; then, you are ready for MD simulation. So for MD is concerned using NAMD, You can not directly run simulation because the parameters and topology of your ligand are unknown to NAMD.

By that we mean that you need to first "Parametrize" your ligand molecules. Now there are two ways to get your parametrization job done. You can do QM calculations using programs like SPARTAN, or you can derive parameters as well as topology of your ligand by analogy using online server Paramchem (https://cgenff.paramchem.org/)

Once you derive topology and parameters for your ligand. you can use LIE (Linear Interaction Energy) method for free energy calculation.

YOu can follow an elementary tutorial in this context at url

http://cinjweb.umdnj.edu/~kerrigje/pdf_files/NAMD-LIE-tutorial.pdf

It is also advised to follow "Parametrizing a novel residue" tutorial at http://www.ks.uiuc.edu/Training/Tutorials/index-all.html#namd

before you proceed to LIE..

hopefully this serves the purpose...

Let me know if you face other difficulty

cheers for NAMD...

Dear Ben,

If you have got the desired pose from docking result and you have a target by hand; then, you are ready for MD simulation. So for MD is concerned using NAMD, You can not directly run simulation because the parameters and topology of your ligand are unknown to NAMD.

By that we mean that you need to first "Parametrize" your ligand molecules. Now there are two ways to get your parametrization job done. You can do QM calculations using programs like SPARTAN, or you can derive parameters as well as topology of your ligand by analogy using online server Paramchem (https://cgenff.paramchem.org/)

Once you derive topology and parameters for your ligand. you can use LIE (Linear Interaction Energy) method for free energy calculation.

YOu can follow an elementary tutorial in this context at url

http://cinjweb.umdnj.edu/~kerrigje/pdf_files/NAMD-LIE-tutorial.pdf

It is also advised to follow "Parametrizing a novel residue" tutorial at http://www.ks.uiuc.edu/Training/Tutorials/index-all.html#namd

before you proceed to LIE..

hopefully this serves the purpose...

Let me know if you face other difficulty

cheers for NAMD...

Thank you very much for the reply. I have been reading the parameterization materials all morning to become familiar with them. I did have one question, though. If some of the ligands are peptides, would it be more appropriate to generate the parameters and topology using psfgen or to use CGENFF? I imagine it would depend on the size of the peptide ligand, but I would appreciate your insights.

Dear ben...

Size don't really matter if your ligand is purely protein you can use psfgen. But if you are using modification in protein or peptides (however small these modifications are) you will have to parametrize them. Paramchem will give high confidence score on ligands which are derived from protein or standard amino acid analogs. you just decide how far your peptide is modified from the original version.

Dear Rohan,

Thank you again for the reply. That helps a lot, and makes sense as I learn more about the parameter files. I appreciate you taking the time to help me. Thanks again!

Dear Rohan,

I am also relatively new to MD. I have generated topology and parameter files for my ligand. How do I proceed from here?? Because I have done MD with NAMD only for a single receptor protein.

If you have a full PDB of your system, CHARMM-GUI can be useful for initial black-boxing.

However, I recommend you study the NAMD manual or GROMACS manual to properly understand how to do this.

http://www.ks.uiuc.edu/Training/Tutorials/namd/namd-tutorial-unix.pdf

Have you managed to extract a structure from AutdockVina?

Christian